From eebb2e01a8a8d67ff27d064e098112941ac83f8f Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Tue, 10 Dec 2024 22:03:20 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/recount3@1edc399fd65aecfd49f18c6649d81da78a36f742=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 24 +- CODE_OF_CONDUCT.html | 18 +- CONTRIBUTING.html | 18 +- SUPPORT.html | 18 +- articles/index.html | 18 +- articles/recount3-quickstart.html | 623 +++++++++++++------------- authors.html | 34 +- index.html | 44 +- news/index.html | 20 +- pkgdown.yml | 7 +- reference/annotation_ext.html | 32 +- reference/annotation_options.html | 28 +- reference/available_projects.html | 46 +- reference/available_samples.html | 44 +- reference/compute_read_counts-1.png | Bin 35952 -> 36195 bytes reference/compute_read_counts-2.png | Bin 38374 -> 38659 bytes reference/compute_read_counts.html | 80 ++-- reference/compute_scale_factors-1.png | Bin 36272 -> 36622 bytes reference/compute_scale_factors.html | 64 +-- reference/create_hub.html | 58 +-- reference/create_rse.html | 352 ++++++++------- reference/create_rse_manual.html | 134 +++--- reference/expand_sra_attributes.html | 60 ++- reference/file_retrieve.html | 60 +-- reference/index.html | 18 +- reference/is_paired_end.html | 54 +-- reference/locate_url.html | 48 +- reference/locate_url_ann.html | 36 +- reference/project_homes.html | 32 +- reference/read_counts.html | 42 +- reference/read_metadata.html | 70 +-- reference/recount3-package.html | 20 +- reference/recount3_cache.html | 34 +- reference/recount3_cache_files.html | 30 +- reference/recount3_cache_rm.html | 34 +- reference/transform_counts-1.png | Bin 36496 -> 36822 bytes reference/transform_counts.html | 62 +-- sitemap.xml | 132 ++---- 38 files changed, 1150 insertions(+), 1244 deletions(-) diff --git a/404.html b/404.html index 93cbbd6..7da0a33 100644 --- a/404.html +++ b/404.html @@ -6,13 +6,7 @@ Page not found (404) • recount3 - - - - - - - + @@ -26,7 +20,7 @@ - +
@@ -52,7 +46,7 @@
- +
@@ -108,16 +102,16 @@

Page not found (404)

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 7aa5681..e2e4c71 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -1,9 +1,9 @@ -Contributor Covenant Code of Conduct • recount3Contributor Covenant Code of Conduct • recount3 - +
@@ -28,7 +28,7 @@
- +
@@ -139,15 +139,15 @@

Attribution -

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 89db0d3..2e8aa21 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -1,9 +1,9 @@ -Contributing to recount3 • recount3Contributing to recount3 • recount3 - +
@@ -28,7 +28,7 @@
- +
@@ -102,15 +102,15 @@

Code of Conduct
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/SUPPORT.html b/SUPPORT.html index e4e5bab..9625341 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -1,9 +1,9 @@ -Getting help with recount3 • recount3Getting help with recount3 • recount3 - +
@@ -28,7 +28,7 @@
- +
@@ -100,15 +100,15 @@

What happens next? -

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/articles/index.html b/articles/index.html index b239ae6..b1683a2 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,9 +1,9 @@ -Articles • recount3Articles • recount3 - +
@@ -28,7 +28,7 @@
- +
@@ -72,15 +72,15 @@

All vignettes

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/articles/recount3-quickstart.html b/articles/recount3-quickstart.html index b7cbc4f..ea67c7d 100644 --- a/articles/recount3-quickstart.html +++ b/articles/recount3-quickstart.html @@ -6,28 +6,20 @@ recount3 quick start guide • recount3 - - - - - - - + - - - +
@@ -53,7 +45,7 @@
- +
@@ -95,9 +87,9 @@

Leonardo University
-

7 May 2023

+

10 December 2024

- Source: vignettes/recount3-quickstart.Rmd + Source: vignettes/recount3-quickstart.Rmd
@@ -108,7 +100,7 @@

7 May 2023

Overview

-

The recount3 +

The recount3 R/Bioconductor package is an interface to the recount3 project. recount3 provides uniformly processed RNA-seq data for hundreds of thousands of samples. The R package makes it possible to easily retrieve this data in @@ -127,51 +119,51 @@

Basics

Installing recount3

R is an open-source statistical environment which can be -easily modified to enhance its functionality via packages. recount3 +easily modified to enhance its functionality via packages. recount3 is a R package available via the Bioconductor repository for packages. R can be installed on any operating system from CRAN after which you can -install recount3 +install recount3 by using the following commands in your R session:

 if (!requireNamespace("BiocManager", quietly = TRUE)) {
     install.packages("BiocManager")
 }
 
-BiocManager::install("recount3")
+BiocManager::install("recount3")
 
 ## Check that you have a valid Bioconductor installation
-BiocManager::valid()
+BiocManager::valid()

You can install the development version from GitHub with:

-BiocManager::install("LieberInstitute/recount3")
+BiocManager::install("LieberInstitute/recount3")

Required knowledge

-

recount3 +

recount3 is based on many other packages and in particular in those that have implemented the infrastructure needed for dealing with RNA-seq data. A -recount3 -user will benefit from being familiar with SummarizedExperiment -to understand the objects recount3 +recount3 +user will benefit from being familiar with SummarizedExperiment +to understand the objects recount3 generates. It might also prove to be highly beneficial to check the

-

Citing recount3 +

Citing recount3

-

We hope that recount3 +

We hope that recount3 will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

@@ -211,11 +203,11 @@ 

Citing citation("recount3") #> To cite package 'recount3' in publications use: #> -#> Collado-Torres L (2023). _Explore and download data from the recount3 +#> Collado-Torres L (2024). _Explore and download data from the recount3 #> project_. doi:10.18129/B9.bioc.recount3 #> <https://doi.org/10.18129/B9.bioc.recount3>, #> https://github.com/LieberInstitute/recount3 - R package version -#> 1.11.2, <http://www.bioconductor.org/packages/recount3>. +#> 1.17.0, <http://www.bioconductor.org/packages/recount3>. #> #> Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, #> Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, @@ -233,7 +225,7 @@

Citing

Quick start

-

After installing recount3 +

After installing recount3 (Wilks, Zheng, Chen, Charles et al., 2021), we need to load the package, which will automatically load the required dependencies.

@@ -250,9 +242,9 @@

Quick start
 ## Find all available human projects
 human_projects <- available_projects()
-#> 2023-05-07 00:13:09.092849 caching file sra.recount_project.MD.gz.
-#> 2023-05-07 00:13:09.470188 caching file gtex.recount_project.MD.gz.
-#> 2023-05-07 00:13:09.797249 caching file tcga.recount_project.MD.gz.
+#> 2024-12-10 22:02:16.504385 caching file sra.recount_project.MD.gz.
+#> 2024-12-10 22:02:16.979699 caching file gtex.recount_project.MD.gz.
+#> 2024-12-10 22:02:17.409176 caching file tcga.recount_project.MD.gz.
 
 ## Find the project you are interested in,
 ## here we use SRP009615 as an example
@@ -263,17 +255,17 @@ 

Quick start## Create a RangedSummarizedExperiment (RSE) object at the gene level rse_gene_SRP009615 <- create_rse(proj_info) -#> 2023-05-07 00:13:14.229616 downloading and reading the metadata. -#> 2023-05-07 00:13:14.522375 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:13:14.84609 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:13:15.174247 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:13:15.538286 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:13:15.860603 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:13:15.935994 downloading and reading the feature information. -#> 2023-05-07 00:13:16.213029 caching file human.gene_sums.G026.gtf.gz. -#> 2023-05-07 00:13:16.729389 downloading and reading the counts: 12 samples across 63856 features. -#> 2023-05-07 00:13:17.001371 caching file sra.gene_sums.SRP009615.G026.gz. -#> 2023-05-07 00:13:17.224353 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:02:21.302687 downloading and reading the metadata. +#> 2024-12-10 22:02:21.727678 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:02:22.207584 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:02:22.723317 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:02:23.143366 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:02:23.612448 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:02:23.669773 downloading and reading the feature information. +#> 2024-12-10 22:02:24.185839 caching file human.gene_sums.G026.gtf.gz. +#> 2024-12-10 22:02:25.199636 downloading and reading the counts: 12 samples across 63856 features. +#> 2024-12-10 22:02:25.565442 caching file sra.gene_sums.SRP009615.G026.gz. +#> 2024-12-10 22:02:25.686254 constructing the RangedSummarizedExperiment (rse) object. ## Explore that RSE object rse_gene_SRP009615 @@ -305,7 +297,7 @@

Quick start## For RPKM, TPM or read outputs, check the details in transform_counts(). assay(rse_gene_SRP009615, "counts") <- transform_counts(rse_gene_SRP009615)

Now you are ready to continue with downstream analysis software.

-

recount3 +

recount3 also supports accessing the BigWig raw coverage files as well as specific study or collection sample metadata. Please continue to the users guide for more detailed information.

@@ -313,7 +305,7 @@

Quick start

Users guide

-

recount3 +

recount3 (Wilks, Zheng, Chen, Charles et al., 2021) provides an interface for downloading the recount3 @@ -327,25 +319,25 @@

Users guideData -source vs collection for details). To get started with recount3, +source vs collection for details). To get started with recount3, you will need to identify the ID for the study of interest from either human or mouse for a particular annotation of interest. Once you have identified study, -data source or collection, and annotation, recount3 +data source or collection, and annotation, recount3 can be used to build a RangedSummarizedExperiment object (Morgan, Obenchain, Hester, and Pagès, 2019) for either gene, exon or exon-exon -junction expression feature data. Furthermore, recount3 +junction expression feature data. Furthermore, recount3 provides access to the coverage BigWig files that can be quantified for -custom set of genomic regions using megadepth. -Furthermore, snapcount +custom set of genomic regions using megadepth. +Furthermore, snapcount allows fast-queries for custom exon-exon junctions and other custom input.

Available data

-

recount3 +

recount3 provides access to most of the recount3 raw files in a form that is R/Bioconductor-friendly. As a summary of the data provided by the recount3 project (Figure @@ -378,7 +370,7 @@

Available databigWig: RNA expression data in raw format at the base-pair coverage resolution. This raw data when coupled with a given annotation can be used to generate gene and exon level counts using -software such as megadepth. +software such as megadepth. It enables exploring the RNA expression landscape in an annotation-agnostic way. @@ -402,7 +394,7 @@

Available dataTerminology

Here we describe some of the common terminology and acronyms used -throughout the rest of the documentation. recount3 +throughout the rest of the documentation. recount3 enables creating RangedSummarizedExperiment objects that contain expression quantitative data (Figure @ref(fig:recountWorkflowFig2)). As a quick overview, some of the main @@ -410,7 +402,7 @@

TerminologySummarizedExperiment +object from SummarizedExperiment (Morgan, Obenchain, Hester, and Pagès, 2019) that contains:

-

recount3 +

recount3 enables accessing data from multiple reference organisms from public projects. To identify these projects, the key terms we use are:

Using transform_counts() you can scale the counts and assign them to the “counts” assays slot to use them in downstream -packages such as DESeq2 and -limma.

+packages such as DESeq2 and +limma.

 ## Once you have your RSE object, you can transform the raw coverage
 ## base-pair coverage counts using transform_counts().
 ## For RPKM, TPM or read outputs, check the details in transform_counts().
 assay(rse_gene_SRP009615, "counts") <- transform_counts(rse_gene_SRP009615)
-

Just like with recount +

Just like with recount for recount2, you can transform the raw base-pair coverage counts (Collado-Torres, @@ -961,13 +953,13 @@

Counts compute_read_counts(), RPKM with recount::getRPKM() or TPM values with recount::getTPM(). Check transform_counts() -from recount3 +from recount3 for more details.

Exon

-

recount3 +

recount3 provides an interface to raw files that go beyond gene counts, as well as other features you might be interested in. For instance, you might want to study expression @@ -980,17 +972,17 @@

Exon proj_info, type = "exon" ) -#> 2023-05-07 00:13:26.019767 downloading and reading the metadata. -#> 2023-05-07 00:13:26.340216 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:13:26.653524 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:13:26.964942 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:13:27.292065 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:13:27.606952 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:13:27.682036 downloading and reading the feature information. -#> 2023-05-07 00:13:27.9505 caching file human.exon_sums.G026.gtf.gz. -#> 2023-05-07 00:13:50.074768 downloading and reading the counts: 12 samples across 1299686 features. -#> 2023-05-07 00:13:50.66939 caching file sra.exon_sums.SRP009615.G026.gz. -#> 2023-05-07 00:13:52.96192 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:02:34.332176 downloading and reading the metadata. +#> 2024-12-10 22:02:34.840852 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:02:35.375054 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:02:35.92474 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:02:36.39949 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:02:36.811251 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:02:36.868213 downloading and reading the feature information. +#> 2024-12-10 22:02:37.291846 caching file human.exon_sums.G026.gtf.gz. +#> 2024-12-10 22:02:55.482803 downloading and reading the counts: 12 samples across 1299686 features. +#> 2024-12-10 22:02:56.08116 caching file sra.exon_sums.SRP009615.G026.gz. +#> 2024-12-10 22:02:57.053694 constructing the RangedSummarizedExperiment (rse) object. ## Explore the resulting RSE exon object rse_exon_SRP009615 @@ -1155,7 +1147,7 @@

Exon

Exon-exon junctions

-

In recount3 +

In recount3 we have also provided the option to create RSE files for exon-exon junctions. Unlike the gene/exon RSE files, only the junctions present in a given project are included in the files, so you’ll have to be more @@ -1171,19 +1163,19 @@

Exon-exon junctionsproj_info, type = "jxn" ) -#> 2023-05-07 00:13:58.486701 downloading and reading the metadata. -#> 2023-05-07 00:13:59.030464 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:13:59.331674 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:13:59.625764 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:13:59.947766 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:14:00.270782 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:14:00.346054 downloading and reading the feature information. -#> 2023-05-07 00:14:00.611637 caching file sra.junctions.SRP009615.ALL.RR.gz. -#> 2023-05-07 00:14:02.320374 downloading and reading the counts: 12 samples across 281448 features. -#> 2023-05-07 00:14:02.580696 caching file sra.junctions.SRP009615.ALL.MM.gz. -#> 2023-05-07 00:14:03.190086 matching exon-exon junction counts with the metadata. -#> 2023-05-07 00:14:03.457154 caching file sra.junctions.SRP009615.ALL.ID.gz. -#> 2023-05-07 00:14:03.589659 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:03:00.658472 downloading and reading the metadata. +#> 2024-12-10 22:03:01.075843 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:03:01.510402 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:03:01.948557 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:03:02.387615 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:03:02.865603 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:03:02.9231 downloading and reading the feature information. +#> 2024-12-10 22:03:03.304952 caching file sra.junctions.SRP009615.ALL.RR.gz. +#> 2024-12-10 22:03:04.561515 downloading and reading the counts: 12 samples across 281448 features. +#> 2024-12-10 22:03:04.959686 caching file sra.junctions.SRP009615.ALL.MM.gz. +#> 2024-12-10 22:03:05.531554 matching exon-exon junction counts with the metadata. +#> 2024-12-10 22:03:05.922275 caching file sra.junctions.SRP009615.ALL.ID.gz. +#> 2024-12-10 22:03:05.989681 constructing the RangedSummarizedExperiment (rse) object. ## Explore the resulting RSE exon-exon junctions object rse_jxn_SRP009615 @@ -1253,10 +1245,10 @@

Exon-exon junctionsBigWig files

Internally we used GenomicFeatures::exonicParts() when -processing all annotations in recount3 +processing all annotations in recount3 instead of GenomicRanges::disjoin() that was used in recount2. We then re-assembled the counts for each -exon/gene to create the count files provided in recount3. +exon/gene to create the count files provided in recount3. However, you might want to exclude the overlapping exonic parts from the counts. If that’s the case or if you are interested in specific regions of the hg38/mm10 genomes, you might want to @@ -1275,27 +1267,27 @@

BigWig filesrtracklayer::import.bw() from R, or other tools such as bwtool that we’ve used in the past 7. Using them, you can compute a coverage matrix for a given set of regions.

-

One new software we developed is megadepth -for which we have provided an R/Bioconductor package interface. megadepth +

One new software we developed is megadepth +for which we have provided an R/Bioconductor package interface. megadepth is faster at accessing BigWig files and is the software we used -internally for generating the recount3 data. megadepth +internally for generating the recount3 data. megadepth provides convenient to use functions for quantifying a set of regions, which might be of interest for co-expression analyses where double counting exonic parts can be problematic.

-

You can also use derfinder -and derfinderPlot +

You can also use derfinder +and derfinderPlot if you are interested in visualizing the base-pair coverage data for a specific region using these BigWig coverage files.

Local files

-

recount3 -depends on BiocFileCache -(Shepherd -and Morgan, 2023) for organizing the raw files and caching them, +

recount3 +depends on BiocFileCache +(Shepherd +and Morgan, 2024) for organizing the raw files and caching them, such that if you use the same file more than once, you only have to -download it once. BiocFileCache +download it once. BiocFileCache will automatically update the file if it detects that the file has changed in the source

If you want to inspect which files you have downloaded or even delete @@ -1375,13 +1367,13 @@

Local files

Your own mirror

-

recount3 +

recount3 functions such as create_rse() have a recount3_url argument that can be changed to point to a mirror or to a path in your computing system. This argument enables -using recount3 +using recount3 with data stored in other locations, or even generated using the same -processing pipeline that was used for recount3 +processing pipeline that was used for recount3 but for your own/private data.

The main documentation website documents how the raw files should be organized in your mirror or for your own data. You can inspect the @@ -1458,14 +1450,14 @@

Project historyDOI: 10.1038/nbt.3838 10.12688/f1000research.12223.1 -recount +recount 2021 recount3 DOI: 10.1186/s13059-021-02533-6 -recount3 +recount3 @@ -1476,9 +1468,9 @@

Date the vignette was generated.

-
#> [1] "2023-05-07 00:14:05 UTC"
+
#> [1] "2024-12-10 22:03:07 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.124 mins
+
#> Time difference of 1.008 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
-#>  version  R version 4.3.0 (2023-04-21)
-#>  os       Ubuntu 22.04.2 LTS
+#>  version  R version 4.4.2 (2024-10-31)
+#>  os       Ubuntu 24.04.1 LTS
 #>  system   x86_64, linux-gnu
 #>  ui       X11
 #>  language en
 #>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2023-05-07
-#>  pandoc   2.19.2 @ /usr/local/bin/ (via rmarkdown)
+#>  date     2024-12-10
+#>  pandoc   3.5 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  package              * version   date (UTC) lib source
-#>  backports              1.4.1     2021-12-13 [1] CRAN (R 4.3.0)
-#>  bibtex                 0.5.1     2023-01-26 [1] RSPM (R 4.3.0)
-#>  Biobase              * 2.60.0    2023-04-25 [1] Bioconductor
-#>  BiocFileCache          2.8.0     2023-04-25 [1] Bioconductor
-#>  BiocGenerics         * 0.46.0    2023-04-25 [1] Bioconductor
-#>  BiocIO                 1.10.0    2023-04-25 [1] Bioconductor
-#>  BiocManager            1.30.20   2023-02-24 [2] CRAN (R 4.3.0)
-#>  BiocParallel           1.34.1    2023-05-05 [1] Bioconductor
-#>  BiocStyle            * 2.28.0    2023-04-25 [1] Bioconductor
-#>  Biostrings             2.68.0    2023-04-25 [1] Bioconductor
-#>  bit                    4.0.5     2022-11-15 [1] CRAN (R 4.3.0)
-#>  bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.3.0)
-#>  bitops                 1.0-7     2021-04-24 [1] CRAN (R 4.3.0)
-#>  blob                   1.2.4     2023-03-17 [1] RSPM (R 4.3.0)
-#>  bookdown               0.33      2023-03-06 [1] RSPM (R 4.3.0)
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-#>  cachem                 1.0.8     2023-05-01 [2] RSPM (R 4.3.0)
-#>  cli                    3.6.1     2023-03-23 [2] RSPM (R 4.3.0)
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@@ -1723,44 +1717,46 @@ 

Reproducibility

Bibliography

-

This vignette was generated using BiocStyle -(Oleś, 2023) +

This vignette was generated using BiocStyle +(Oleś, 2024) with knitr (Xie, 2014) and rmarkdown (Allaire, Xie, Dervieux, -McPherson et al., 2023) running behind the scenes.

+McPherson et al., 2024) running behind the scenes.

Citations made with knitcitations (Boettiger, 2021).

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[2] S. Balcome. interactiveDisplayBase: Base package for enabling powerful shiny web displays of Bioconductor objects. R package -version 1.38.0. 2023. DOI: 10.18129/B9.bioc.interactiveDisplayBase. https://bioconductor.org/packages/interactiveDisplayBase.

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[3] D. Bates, M. Maechler, and M. Jagan. Matrix: Sparse and Dense -Matrix Classes and Methods. R package version 1.5-4. 2023. https://CRAN.R-project.org/package=Matrix.

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[4] H. Bengtsson. R.utils: Various Programming Utilities. R -package version 2.12.2. 2022. https://CRAN.R-project.org/package=R.utils.

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[5] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown +version 1.44.0. 2024. DOI: 10.18129/B9.bioc.interactiveDisplayBase. https://bioconductor.org/packages/interactiveDisplayBase.

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[3] T. Barrett, M. Dowle, A. Srinivasan, J. Gorecki, et +al. data.table: Extension of data.frame. R package +version 1.16.4, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table. 2024. https://r-datatable.com.

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[4] D. Bates, M. Maechler, and M. Jagan. Matrix: Sparse and Dense +Matrix Classes and Methods. R package version 1.7-1. 2024. https://CRAN.R-project.org/package=Matrix.

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[5] H. Bengtsson. R.utils: Various Programming Utilities. R +package version 2.12.3, https://github.com/HenrikBengtsson/R.utils. 2023. https://henrikbengtsson.github.io/R.utils/.

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[6] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.12. 2021. https://github.com/cboettig/knitcitations.

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[6] L. Collado-Torres. Explore and download data from the +

[7] L. Collado-Torres. Explore and download data from the recount3 project. https://github.com/LieberInstitute/recount3 - R package -version 1.11.2. 2023. DOI: 10.18129/B9.bioc.recount3. http://www.bioconductor.org/packages/recount3.

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[7] L. Collado-Torres, A. Nellore, and A. E. Jaffe. “recount +version 1.17.0. 2024. DOI: 10.18129/B9.bioc.recount3. http://www.bioconductor.org/packages/recount3.

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[8] L. Collado-Torres, A. Nellore, and A. E. Jaffe. “recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor [version 1; referees: 1 approved, 2 approved with reservations]”. In: F1000Research (2017). DOI: 10.12688/f1000research.12223.1. https://f1000research.com/articles/6-1558/v1.

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[8] L. Collado-Torres, A. Nellore, K. Kammers, S. E. Ellis, et +

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@@ -1781,28 +1777,29 @@

Bibliographyhttps://bioconductor.org/packages/BiocStyle.

[19] H. Pagès, M. Lawrence, and P. Aboyoun. S4Vectors: Foundation of vector-like and list-like containers in Bioconductor. R package -version 0.38.1. 2023. DOI: 10.18129/B9.bioc.S4Vectors. https://bioconductor.org/packages/S4Vectors.

+version 0.44.0. 2024. DOI: 10.18129/B9.bioc.S4Vectors. https://bioconductor.org/packages/S4Vectors.

[20] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, -2023. https://www.R-project.org/.

+2024. https://www.R-project.org/.

[21] A. Razmara, S. E. Ellis, D. J. Sokolowski, S. Davis, et al. “recount-brain: a curated repository of human brain RNA-seq datasets metadata”. In: bioRxiv (2019). DOI: 10.1101/618025. https://doi.org/10.1101/618025.

[22] L. Shepherd and M. Morgan. BiocFileCache: Manage Files -Across Sessions. R package version 2.8.0. 2023. DOI: +Across Sessions. R package version 2.14.0. 2024. DOI: 10.18129/B9.bioc.BiocFileCache. https://bioconductor.org/packages/BiocFileCache.

[23] H. Wickham. httr: Tools for Working with URLs and HTTP. -https://httr.r-lib.org/, https://github.com/r-lib/httr. 2023.

+R package version 1.4.7, https://github.com/r-lib/httr. 2023. https://httr.r-lib.org/.

[24] H. Wickham. pryr: Tools for Computing on the Language. R package version 0.1.6. 2023. https://github.com/hadley/pryr.

[25] H. Wickham. “testthat: Get Started with Testing”. In: The R Journal 3 (2011), pp. 5-10. https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf.

[26] H. Wickham, W. Chang, R. Flight, K. Müller, et -al. sessioninfo: R Session Information. https://github.com/r-lib/sessioninfo#readme, https://r-lib.github.io/sessioninfo/. 2021.

+al. sessioninfo: R Session Information. R package version +1.2.2, https://r-lib.github.io/sessioninfo/. 2021. https://github.com/r-lib/sessioninfo#readme.

[27] C. Wilks, S. C. Zheng, F. Y. Chen, R. Charles, et al. “recount3: summaries and queries for large-scale RNA-seq expression and splicing”. In: Genome Biol (2021). DOI: 10.1186/s13059-021-02533-6. https://doi.org/10.1186/s13059-021-02533-6.

@@ -1832,9 +1829,7 @@

Bibliography - -

+ @@ -1847,16 +1842,16 @@

Bibliography

-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/authors.html b/authors.html index 263c147..4e396e0 100644 --- a/authors.html +++ b/authors.html @@ -1,9 +1,9 @@ -Authors and Citation • recount3Authors and Citation • recount3 - +
@@ -28,7 +28,7 @@
- +
- +
-

Site built with pkgdown 2.0.7.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/index.html b/index.html index 9efa32f..1b66f96 100644 --- a/index.html +++ b/index.html @@ -6,24 +6,14 @@ Explore and download data from the recount3 project • recount3 - - - - - - - + - + - +
@@ -57,7 +47,7 @@
- +
@@ -109,7 +99,7 @@

Installation instructions install.packages("BiocManager") } -BiocManager::install("recount3")

+BiocManager::install("recount3")

Citation @@ -185,28 +175,28 @@

Project history - + Year Phase Main references R/Bioconductor - + 2011 ReCount DOI: 10.1186/1471-2105-12-449 none - + 2017 recount2 DOI: 10.1038/nbt.3838 10.12688/f1000research.12223.1 recount - + 2021 recount3 DOI: 10.1186/s13059-021-02533-6 @@ -238,7 +228,7 @@

Teams involved - + @@ -309,7 +299,7 @@

Dev status

  • Bioc last commit
  • Bioc dependencies
  • Codecov test coverage
  • -
  • R build status
  • +
  • R build status
  • GitHub issues
  • GitHub pulls
  • @@ -326,16 +316,16 @@

    Dev status

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/news/index.html b/news/index.html index 197dc11..16eea24 100644 --- a/news/index.html +++ b/news/index.html @@ -1,9 +1,9 @@ -Changelog • recount3Changelog • recount3 - +
    @@ -28,7 +28,7 @@
    - +
    @@ -134,15 +134,15 @@
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/pkgdown.yml b/pkgdown.yml index 852a299..4c2a763 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,7 +1,6 @@ -pandoc: 2.19.2 -pkgdown: 2.0.7 +pandoc: '3.5' +pkgdown: 2.1.1 pkgdown_sha: ~ articles: recount3-quickstart: recount3-quickstart.html -last_built: 2023-05-07T00:09Z - +last_built: 2024-12-10T21:59Z diff --git a/reference/annotation_ext.html b/reference/annotation_ext.html index 5670302..94b079e 100644 --- a/reference/annotation_ext.html +++ b/reference/annotation_ext.html @@ -1,10 +1,10 @@ -Obtain the file extension for a given organism and annotation — annotation_ext • recount3Obtain the file extension for a given organism and annotation — annotation_ext • recount3 - +
    @@ -29,7 +29,7 @@
    - +
    @@ -73,25 +73,25 @@

    Obtain the file extension for a given organism and annotation

    Arguments

    -
    organism
    + + +
    organism

    A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".

    -
    annotation
    +
    annotation

    A character(1) specifying which annotation you want to use.

    Value

    - - -

    A character(1) with the annotation file extension to be used.

    +

    A character(1) with the annotation file extension to be used.

    See also

    -

    Other internal functions for accessing the recount3 data: +

    Other internal functions for accessing the recount3 data: create_rse_manual(), file_retrieve(), locate_url_ann(), @@ -126,15 +126,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/annotation_options.html b/reference/annotation_options.html index 42334cd..d4bf896 100644 --- a/reference/annotation_options.html +++ b/reference/annotation_options.html @@ -1,10 +1,10 @@ -List available annotation options for a given organism — annotation_options • recount3List available annotation options for a given organism — annotation_options • recount3 - +
    @@ -29,7 +29,7 @@
    - +
    @@ -70,16 +70,16 @@

    List available annotation options for a given organism

    Arguments

    -
    organism
    + + +
    organism

    A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".

    Value

    - - -

    A character() vector with the supported annotation options for the +

    A character() vector with the supported annotation options for the given organism.

    @@ -105,15 +105,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/available_projects.html b/reference/available_projects.html index e2e0f99..b433ef7 100644 --- a/reference/available_projects.html +++ b/reference/available_projects.html @@ -1,9 +1,9 @@ -List available projects in recount3 — available_projects • recount3List available projects in recount3 — available_projects • recount3 - +
    @@ -28,7 +28,7 @@
    - +
    @@ -73,12 +73,14 @@

    List available projects in recount3

    Arguments

    -
    organism
    + + +
    organism

    A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".

    -
    recount3_url
    +
    recount3_url

    A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be @@ -89,13 +91,13 @@

    Arguments

    you have a favorite mirror.

    -
    bfc
    +
    bfc

    A BiocFileCache-class object where the files will be cached to, typically created by recount3_cache().

    -
    available_homes
    +
    available_homes

    A character() vector with the available project homes for the given recount3_url. If you use a non-standard recount3_url, you will likely need to specify manually the valid values for available_homes.

    @@ -103,9 +105,7 @@

    Arguments

    Value

    - - -

    A data.frame() with the project ID (project), the organism, the +

    A data.frame() with the project ID (project), the organism, the file_source from where the data was accessed, the recount3 project home location (project_home), the project project_type that differentiates between data_sources and compilations, @@ -117,9 +117,9 @@

    Examples

    
     ## Find all the human projects
     human_projects <- available_projects()
    -#> 2023-05-07 00:10:05.710375 caching file sra.recount_project.MD.gz.
    -#> 2023-05-07 00:10:06.059883 caching file gtex.recount_project.MD.gz.
    -#> 2023-05-07 00:10:06.403144 caching file tcga.recount_project.MD.gz.
    +#> 2024-12-10 21:59:18.606342 caching file sra.recount_project.MD.gz.
    +#> 2024-12-10 21:59:19.057311 caching file gtex.recount_project.MD.gz.
    +#> 2024-12-10 21:59:19.494311 caching file tcga.recount_project.MD.gz.
     
     ## Explore the results
     dim(human_projects)
    @@ -175,7 +175,7 @@ 

    Examples

    ## Find all the mouse projects mouse_projects <- available_projects(organism = "mouse") -#> 2023-05-07 00:10:12.289013 caching file sra.recount_project.MD.gz. +#> 2024-12-10 21:59:24.865845 caching file sra.recount_project.MD.gz. ## Explore the results dim(mouse_projects) @@ -203,7 +203,7 @@

    Examples

    #> sra #> 10088 -if (FALSE) { +if (FALSE) { # \dontrun{ ## Use with a custom recount3_url: available_projects( recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3test", @@ -216,7 +216,7 @@

    Examples

    available_projects( recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3test" ) -} +} # }
    @@ -231,15 +231,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/available_samples.html b/reference/available_samples.html index 2889a81..6c0b0c6 100644 --- a/reference/available_samples.html +++ b/reference/available_samples.html @@ -1,11 +1,11 @@ -List available samples in recount3 — available_samples • recount3List available samples in recount3 — available_samples • recount3 - +
    @@ -30,7 +30,7 @@
    - +
    @@ -78,12 +78,14 @@

    List available samples in recount3

    Arguments

    -
    organism
    + + +
    organism

    A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".

    -
    recount3_url
    +
    recount3_url

    A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be @@ -94,18 +96,18 @@

    Arguments

    you have a favorite mirror.

    -
    bfc
    +
    bfc

    A BiocFileCache-class object where the files will be cached to, typically created by recount3_cache().

    -
    verbose
    +
    verbose

    A logical(1) indicating whether to show messages with updates.

    -
    available_homes
    +
    available_homes

    A character() vector with the available project homes for the given recount3_url. If you use a non-standard recount3_url, you will likely need to specify manually the valid values for available_homes.

    @@ -113,9 +115,7 @@

    Arguments

    Value

    - - -

    A data.frame() with the sample ID used by the original source of +

    A data.frame() with the sample ID used by the original source of the data (external_id), the project ID (project), the organism, the file_source from where the data was accessed, the date the sample was processed (date_processed) in YYYY-MM-DD format, @@ -128,9 +128,9 @@

    Examples

    
     ## Find all the human samples available from recount3
     human_samples <- available_samples()
    -#> 2023-05-07 00:10:16.352644 caching file sra.recount_project.MD.gz.
    -#> 2023-05-07 00:10:16.658074 caching file gtex.recount_project.MD.gz.
    -#> 2023-05-07 00:10:17.013503 caching file tcga.recount_project.MD.gz.
    +#> 2024-12-10 21:59:28.135471 caching file sra.recount_project.MD.gz.
    +#> 2024-12-10 21:59:28.590343 caching file gtex.recount_project.MD.gz.
    +#> 2024-12-10 21:59:28.996636 caching file tcga.recount_project.MD.gz.
     dim(human_samples)
     #> [1] 347005      7
     head(human_samples)
    @@ -165,7 +165,7 @@ 

    Examples

    ## Find all the mouse samples available from recount3 mouse_samples <- available_samples("mouse") -#> 2023-05-07 00:10:19.163851 caching file sra.recount_project.MD.gz. +#> 2024-12-10 21:59:31.579098 caching file sra.recount_project.MD.gz. dim(mouse_samples) #> [1] 416859 7 head(mouse_samples) @@ -203,15 +203,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

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zNPdu2sECywmP?TLd&iRcvs&SI?g0i#s@U7HB90KXIZhA#4e~@y@9m;EevW()i-~04 ztnF6aU3R~tLeuzp)8JK6lN*QypyII$t -Compute read counts — compute_read_counts • recount3Compute read counts — compute_read_counts • recount3 - +
    @@ -30,7 +30,7 @@
    - +
    @@ -76,18 +76,20 @@

    Compute read counts

    Arguments

    -
    rse
    + + +
    rse

    A RangedSummarizedExperiment-class created by create_rse().

    -
    round
    +
    round

    A logical(1) specifying whether to round the transformed counts or not.

    -
    avg_mapped_read_length
    +
    avg_mapped_read_length

    A character(1) specifying the metdata column name that contains the average fragment length after aligning. This is typically twice the average read length for paired-end reads.

    @@ -95,9 +97,7 @@

    Arguments

    Value

    - - -

    A matrix() with the read counts. By default this function uses +

    A matrix() with the read counts. By default this function uses the average read length to the QC annotation.

    @@ -117,7 +117,7 @@

    References

    See also

    -

    Other count transformation functions: +

    Other count transformation functions: compute_scale_factors(), is_paired_end(), transform_counts()

    @@ -128,17 +128,17 @@

    Examples

    
     ## Create a RSE object at the gene level
     rse_gene_SRP009615 <- create_rse_manual("SRP009615")
    -#> 2023-05-07 00:10:22.027918 downloading and reading the metadata.
    -#> 2023-05-07 00:10:22.332659 caching file sra.sra.SRP009615.MD.gz.
    -#> 2023-05-07 00:10:22.640917 caching file sra.recount_project.SRP009615.MD.gz.
    -#> 2023-05-07 00:10:22.966372 caching file sra.recount_qc.SRP009615.MD.gz.
    -#> 2023-05-07 00:10:23.315081 caching file sra.recount_seq_qc.SRP009615.MD.gz.
    -#> 2023-05-07 00:10:23.628464 caching file sra.recount_pred.SRP009615.MD.gz.
    -#> 2023-05-07 00:10:23.704635 downloading and reading the feature information.
    -#> 2023-05-07 00:10:23.983416 caching file human.gene_sums.G026.gtf.gz.
    -#> 2023-05-07 00:10:24.519525 downloading and reading the counts: 12 samples across 63856 features.
    -#> 2023-05-07 00:10:24.830053 caching file sra.gene_sums.SRP009615.G026.gz.
    -#> 2023-05-07 00:10:25.069605 constructing the RangedSummarizedExperiment (rse) object.
    +#> 2024-12-10 21:59:33.741533 downloading and reading the metadata.
    +#> 2024-12-10 21:59:34.173184 caching file sra.sra.SRP009615.MD.gz.
    +#> 2024-12-10 21:59:34.674165 caching file sra.recount_project.SRP009615.MD.gz.
    +#> 2024-12-10 21:59:35.123934 caching file sra.recount_qc.SRP009615.MD.gz.
    +#> 2024-12-10 21:59:35.538204 caching file sra.recount_seq_qc.SRP009615.MD.gz.
    +#> 2024-12-10 21:59:36.030442 caching file sra.recount_pred.SRP009615.MD.gz.
    +#> 2024-12-10 21:59:36.086495 downloading and reading the feature information.
    +#> 2024-12-10 21:59:36.525859 caching file human.gene_sums.G026.gtf.gz.
    +#> 2024-12-10 21:59:36.999886 downloading and reading the counts: 12 samples across 63856 features.
    +#> 2024-12-10 21:59:37.397925 caching file sra.gene_sums.SRP009615.G026.gz.
    +#> 2024-12-10 21:59:38.204639 constructing the RangedSummarizedExperiment (rse) object.
     colSums(compute_read_counts(rse_gene_SRP009615)) / 1e6
     #> SRR387777 SRR387778 SRR387779 SRR387780 SRR389079 SRR389080 SRR389081 SRR389082 
     #>  21.29962  23.66484  32.62525  25.46085  41.48717  28.05485  17.78092  15.46669 
    @@ -147,17 +147,17 @@ 

    Examples

    ## Create a RSE object at the gene level rse_gene_DRP000499 <- create_rse_manual("DRP000499") -#> 2023-05-07 00:10:25.147308 downloading and reading the metadata. -#> 2023-05-07 00:10:25.417019 caching file sra.sra.DRP000499.MD.gz. -#> 2023-05-07 00:10:25.734304 caching file sra.recount_project.DRP000499.MD.gz. -#> 2023-05-07 00:10:26.051436 caching file sra.recount_qc.DRP000499.MD.gz. -#> 2023-05-07 00:10:26.365882 caching file sra.recount_seq_qc.DRP000499.MD.gz. -#> 2023-05-07 00:10:26.72776 caching file sra.recount_pred.DRP000499.MD.gz. -#> 2023-05-07 00:10:26.803488 downloading and reading the feature information. -#> 2023-05-07 00:10:27.079844 caching file human.gene_sums.G026.gtf.gz. -#> 2023-05-07 00:10:27.552718 downloading and reading the counts: 21 samples across 63856 features. -#> 2023-05-07 00:10:27.855395 caching file sra.gene_sums.DRP000499.G026.gz. -#> 2023-05-07 00:10:28.09871 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 21:59:38.265827 downloading and reading the metadata. +#> 2024-12-10 21:59:38.65617 caching file sra.sra.DRP000499.MD.gz. +#> 2024-12-10 21:59:39.062821 caching file sra.recount_project.DRP000499.MD.gz. +#> 2024-12-10 21:59:39.504425 caching file sra.recount_qc.DRP000499.MD.gz. +#> 2024-12-10 21:59:39.951666 caching file sra.recount_seq_qc.DRP000499.MD.gz. +#> 2024-12-10 21:59:40.406476 caching file sra.recount_pred.DRP000499.MD.gz. +#> 2024-12-10 21:59:40.461081 downloading and reading the feature information. +#> 2024-12-10 21:59:40.850277 caching file human.gene_sums.G026.gtf.gz. +#> 2024-12-10 21:59:41.190182 downloading and reading the counts: 21 samples across 63856 features. +#> 2024-12-10 21:59:41.540814 caching file sra.gene_sums.DRP000499.G026.gz. +#> 2024-12-10 21:59:41.685596 constructing the RangedSummarizedExperiment (rse) object. colSums(compute_read_counts(rse_gene_DRP000499)) / 1e6 #> DRR001622 DRR001623 DRR001624 DRR001625 DRR001626 DRR001627 DRR001628 DRR001629 #> 10.952140 7.995718 11.874082 NaN 7.518984 11.272031 53.412769 27.539984 @@ -186,7 +186,7 @@

    Examples

    ## Repeat for DRP000499, a paired-end study recount::download_study("DRP000499", outdir = tempdir()) -#> 2023-05-07 00:10:31.92353 downloading file rse_gene.Rdata to /tmp/RtmpAxQcvh +#> 2024-12-10 21:59:44.033302 downloading file rse_gene.Rdata to /tmp/Rtmp4b1Pjm load(file.path(tempdir(), "rse_gene.Rdata"), verbose = TRUE) #> Loading objects: #> rse_gene @@ -216,15 +216,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

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b/reference/compute_scale_factors.html index dd07bb2..1441373 100644 --- a/reference/compute_scale_factors.html +++ b/reference/compute_scale_factors.html @@ -1,11 +1,11 @@ -Compute count scaling factors — compute_scale_factors • recount3Compute count scaling factors — compute_scale_factors • recount3 - +
    @@ -30,7 +30,7 @@
    - +
    @@ -81,14 +81,16 @@

    Compute count scaling factors

    Arguments

    -
    x
    + + +
    x

    Either a RangedSummarizedExperiment-class created by create_rse() or the sample metadata created by read_metadata().

    -
    by
    +
    by

    Either auc or mapped_reads. If set to auc it will compute the scaling factor by the total coverage of the sample. That is, the area under the curve (AUC) of the coverage. If set to mapped_reads it @@ -96,50 +98,48 @@

    Arguments

    whether the library was paired-end or not, and the desired read length (L).

    -
    targetSize
    +
    targetSize

    A numeric(1) specifying the target library size in number of single end reads.

    -
    L
    +
    L

    A integer(1) specifying the target read length. It is only used when by = 'mapped_reads' since it cancels out in the calculation when using by = 'auc'.

    -
    auc
    +
    auc

    A character(1) specifying the metadata column name that contains the area under the coverage (AUC). Note that there are several possible AUC columns provided in the sample metadata generated by create_rse().

    -
    avg_mapped_read_length
    +
    avg_mapped_read_length

    A character(1) specifying the metdata column name that contains the average fragment length after aligning. This is typically twice the average read length for paired-end reads.

    -
    mapped_reads
    +
    mapped_reads

    A character(1) specifying the metadata column name that contains the number of mapped reads.

    -
    paired_end
    +
    paired_end

    A logical() vector specifying whether each sample is paired-end or not.

    Value

    - - -

    A numeric() with the sample scale factors that are used by +

    A numeric() with the sample scale factors that are used by transform_counts().

    See also

    -

    Other count transformation functions: +

    Other count transformation functions: compute_read_counts(), is_paired_end(), transform_counts()

    @@ -157,11 +157,11 @@

    Examples

    ) ) ) -#> 2023-05-07 00:10:35.994636 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:10:36.306626 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:10:36.62662 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:10:36.949452 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:10:37.28351 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 21:59:47.229737 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 21:59:47.652743 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 21:59:48.079769 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 21:59:48.512771 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 21:59:48.950279 caching file sra.recount_pred.SRP009615.MD.gz. ## Compute the scaling factors compute_scale_factors(SRP009615_meta, by = "auc") @@ -184,11 +184,11 @@

    Examples

    ) ) ) -#> 2023-05-07 00:10:37.655073 caching file sra.sra.DRP000499.MD.gz. -#> 2023-05-07 00:10:37.981805 caching file sra.recount_project.DRP000499.MD.gz. -#> 2023-05-07 00:10:38.304785 caching file sra.recount_qc.DRP000499.MD.gz. -#> 2023-05-07 00:10:38.635387 caching file sra.recount_seq_qc.DRP000499.MD.gz. -#> 2023-05-07 00:10:38.999166 caching file sra.recount_pred.DRP000499.MD.gz. +#> 2024-12-10 21:59:49.407388 caching file sra.sra.DRP000499.MD.gz. +#> 2024-12-10 21:59:49.837336 caching file sra.recount_project.DRP000499.MD.gz. +#> 2024-12-10 21:59:50.328804 caching file sra.recount_qc.DRP000499.MD.gz. +#> 2024-12-10 21:59:50.742202 caching file sra.recount_seq_qc.DRP000499.MD.gz. +#> 2024-12-10 21:59:51.272496 caching file sra.recount_pred.DRP000499.MD.gz. ## Compute the scaling factors compute_scale_factors(DRP000499_meta, by = "auc") @@ -241,15 +241,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/create_hub.html b/reference/create_hub.html index c757b1e..b599c82 100644 --- a/reference/create_hub.html +++ b/reference/create_hub.html @@ -1,5 +1,5 @@ -Create UCSC track hub for BigWig files — create_hub • recount3Create UCSC track hub for BigWig files — create_hub • recount3 - +
    @@ -32,7 +32,7 @@
    - +
    @@ -87,44 +87,46 @@

    Create UCSC track hub for BigWig files

    Arguments

    -
    x
    + + +
    x

    A data.frame created with available_samples() that has typically been subset to a specific project ID from a given organism.

    -
    output_dir
    +
    output_dir

    A character(1) with the output directory.

    -
    hub_name
    +
    hub_name

    A character(1) with the UCSC track hub name you want to display.

    -
    email
    +
    email

    A character(1) with the email used for the UCSC track hub.

    -
    show_max
    +
    show_max

    An integer(1) with the number of BigWig tracks to show by default in the UCSC track hub. We recommend a single digit number.

    -
    hub_short_label
    +
    hub_short_label

    A character(1) with the UCSC track hub short label.

    -
    hub_long_label
    +
    hub_long_label

    A character(1) with the UCSC track hub long label.

    -
    hub_description_url
    +
    hub_description_url

    A character(1) with the URL to an html file that will describe the UCSC track hub to users.

    -
    recount3_url
    +
    recount3_url

    A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be @@ -137,9 +139,7 @@

    Arguments

    Value

    - - -

    A directory at output_dir with the files needed for a UCSC +

    A directory at output_dir with the files needed for a UCSC track hub.

    @@ -154,7 +154,7 @@

    Examples

    
     ## Find all the mouse samples available from recount3
     mouse_samples <- available_samples("mouse")
    -#> 2023-05-07 00:10:39.698728 caching file sra.recount_project.MD.gz.
    +#> 2024-12-10 21:59:52.058949 caching file sra.recount_project.MD.gz.
     
     ## Subset to project DRP001299
     info_DRP001299 <- subset(mouse_samples, project == "DRP001299")
    @@ -164,9 +164,9 @@ 

    Examples

    ## List the files created by create_hub() hub_files <- list.files(hub_dir, full.names = TRUE, recursive = TRUE) hub_files -#> [1] "/tmp/RtmpAxQcvh/DRP001299/genomes.txt" -#> [2] "/tmp/RtmpAxQcvh/DRP001299/hub.txt" -#> [3] "/tmp/RtmpAxQcvh/DRP001299/mm10/trackDb.txt" +#> [1] "/tmp/Rtmp4b1Pjm/DRP001299/genomes.txt" +#> [2] "/tmp/Rtmp4b1Pjm/DRP001299/hub.txt" +#> [3] "/tmp/Rtmp4b1Pjm/DRP001299/mm10/trackDb.txt" ## Check the files contents sapply(hub_files, function(x) { @@ -259,13 +259,13 @@

    Examples

    #> type bigWig #> visibility hide #> autoScale on -#> $`/tmp/RtmpAxQcvh/DRP001299/genomes.txt` +#> $`/tmp/Rtmp4b1Pjm/DRP001299/genomes.txt` #> NULL #> -#> $`/tmp/RtmpAxQcvh/DRP001299/hub.txt` +#> $`/tmp/Rtmp4b1Pjm/DRP001299/hub.txt` #> NULL #> -#> $`/tmp/RtmpAxQcvh/DRP001299/mm10/trackDb.txt` +#> $`/tmp/Rtmp4b1Pjm/DRP001299/mm10/trackDb.txt` #> NULL #> @@ -287,15 +287,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/create_rse.html b/reference/create_rse.html index cd37771..dabdb7c 100644 --- a/reference/create_rse.html +++ b/reference/create_rse.html @@ -1,5 +1,5 @@ -Create a recount3 RangedSummarizedExperiment gene or exon object — create_rse • recount3Create a recount3 RangedSummarizedExperiment gene or exon object — create_rse • recount3 - +
    @@ -32,7 +32,7 @@
    - +
    @@ -84,36 +84,38 @@

    Create a recount3 RangedSummarizedExperiment gene or exon object

    Arguments

    -
    project_info
    + + +
    project_info

    A data.frame() with one row that contains the information for the project you are interested in. You can find which project to work on using available_projects().

    -
    type
    +
    type

    A character(1) specifying whether you want to access gene, exon, or exon-exon junction counts.

    -
    annotation
    +
    annotation

    A character(1) specifying which annotation you want to download. Only used when type is either gene or exon.

    -
    bfc
    +
    bfc

    A BiocFileCache-class object where the files will be cached to, typically created by recount3_cache().

    -
    jxn_format
    +
    jxn_format

    A character(1) specifying whether the exon-exon junction files are derived from all the reads (ALL) or only the uniquely mapping read counts (UNIQUE). Note that UNIQUE is only available for some projects: GTEx and TCGA for human.

    -
    recount3_url
    +
    recount3_url

    A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be @@ -124,20 +126,16 @@

    Arguments

    you have a favorite mirror.

    -
    verbose
    +
    verbose

    A logical(1) indicating whether to show messages with updates.

    Value

    - - -

    A -RangedSummarizedExperiment-class

    - - -

    object.

    +

    A +RangedSummarizedExperiment-class +object.

    @@ -145,9 +143,9 @@

    Examples

    
     ## Find all available human projects
     human_projects <- available_projects()
    -#> 2023-05-07 00:10:43.158444 caching file sra.recount_project.MD.gz.
    -#> 2023-05-07 00:10:43.471854 caching file gtex.recount_project.MD.gz.
    -#> 2023-05-07 00:10:43.842242 caching file tcga.recount_project.MD.gz.
    +#> 2024-12-10 21:59:55.053792 caching file sra.recount_project.MD.gz.
    +#> 2024-12-10 21:59:55.586099 caching file gtex.recount_project.MD.gz.
    +#> 2024-12-10 21:59:55.986213 caching file tcga.recount_project.MD.gz.
     
     ## Find the project you are interested in
     proj_info <- subset(
    @@ -157,17 +155,17 @@ 

    Examples

    ## Create a RSE object at the gene level rse_gene_SRP009615 <- create_rse(proj_info) -#> 2023-05-07 00:10:47.629258 downloading and reading the metadata. -#> 2023-05-07 00:10:47.93515 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:10:48.253151 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:10:48.573828 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:10:48.891872 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:10:49.203151 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:10:49.285469 downloading and reading the feature information. -#> 2023-05-07 00:10:49.557602 caching file human.gene_sums.G026.gtf.gz. -#> 2023-05-07 00:10:50.043949 downloading and reading the counts: 12 samples across 63856 features. -#> 2023-05-07 00:10:50.311859 caching file sra.gene_sums.SRP009615.G026.gz. -#> 2023-05-07 00:10:50.493249 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 21:59:59.002098 downloading and reading the metadata. +#> 2024-12-10 21:59:59.38987 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 21:59:59.883274 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:00.299241 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:00.75216 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:01.197772 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:01.269633 downloading and reading the feature information. +#> 2024-12-10 22:00:01.639778 caching file human.gene_sums.G026.gtf.gz. +#> 2024-12-10 22:00:02.125041 downloading and reading the counts: 12 samples across 63856 features. +#> 2024-12-10 22:00:02.499416 caching file sra.gene_sums.SRP009615.G026.gz. +#> 2024-12-10 22:00:02.633623 constructing the RangedSummarizedExperiment (rse) object. ## Explore the resulting RSE gene object rse_gene_SRP009615 @@ -185,13 +183,13 @@

    Examples

    ## Information about how this RSE object was made metadata(rse_gene_SRP009615) #> $time_created -#> [1] "2023-05-07 00:10:50 UTC" +#> [1] "2024-12-10 22:00:02 UTC" #> #> $recount3_version #> package ondiskversion loadedversion path -#> recount3 recount3 1.11.2 1.11.2 /__w/_temp/Library/recount3 +#> recount3 recount3 1.17.0 1.17.0 /__w/_temp/Library/recount3 #> loadedpath attached is_base date source -#> recount3 /__w/_temp/Library/recount3 TRUE FALSE 2023-05-07 Bioconductor +#> recount3 /__w/_temp/Library/recount3 TRUE FALSE 2024-12-10 Bioconductor #> md5ok library #> recount3 NA /__w/_temp/Library #> @@ -526,17 +524,17 @@

    Examples

    proj_info, annotation = "fantom6_cat" ) -#> 2023-05-07 00:10:53.784254 downloading and reading the metadata. -#> 2023-05-07 00:10:54.069448 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:10:54.378223 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:10:54.715142 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:10:55.034494 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:10:55.34915 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:10:55.432427 downloading and reading the feature information. -#> 2023-05-07 00:10:55.710198 caching file human.gene_sums.F006.gtf.gz. -#> 2023-05-07 00:10:56.156776 downloading and reading the counts: 12 samples across 124047 features. -#> 2023-05-07 00:10:56.42205 caching file sra.gene_sums.SRP009615.F006.gz. -#> 2023-05-07 00:10:56.708977 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:06.362463 downloading and reading the metadata. +#> 2024-12-10 22:00:06.841102 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:07.239131 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:07.668843 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:08.097587 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:08.559095 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:08.620419 downloading and reading the feature information. +#> 2024-12-10 22:00:09.024966 caching file human.gene_sums.F006.gtf.gz. +#> 2024-12-10 22:00:09.335933 downloading and reading the counts: 12 samples across 124047 features. +#> 2024-12-10 22:00:09.716042 caching file sra.gene_sums.SRP009615.F006.gz. +#> 2024-12-10 22:00:09.942281 constructing the RangedSummarizedExperiment (rse) object. rowRanges(rse_gene_SRP009615_fantom6_cat) #> GRanges object with 124047 ranges and 5 metadata columns: #> seqnames ranges strand | source type @@ -573,17 +571,17 @@

    Examples

    proj_info, annotation = "refseq" ) -#> 2023-05-07 00:10:56.746102 downloading and reading the metadata. -#> 2023-05-07 00:10:57.029173 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:10:57.349174 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:10:57.664051 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:10:57.98792 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:10:58.3011 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:10:58.384231 downloading and reading the feature information. -#> 2023-05-07 00:10:58.64316 caching file human.gene_sums.R109.gtf.gz. -#> 2023-05-07 00:10:59.200787 downloading and reading the counts: 12 samples across 54042 features. -#> 2023-05-07 00:10:59.469325 caching file sra.gene_sums.SRP009615.R109.gz. -#> 2023-05-07 00:10:59.701913 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:09.97089 downloading and reading the metadata. +#> 2024-12-10 22:00:10.359785 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:10.788713 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:11.21541 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:11.64989 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:12.038071 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:12.099174 downloading and reading the feature information. +#> 2024-12-10 22:00:12.498656 caching file human.gene_sums.R109.gtf.gz. +#> 2024-12-10 22:00:13.089154 downloading and reading the counts: 12 samples across 54042 features. +#> 2024-12-10 22:00:13.578814 caching file sra.gene_sums.SRP009615.R109.gz. +#> 2024-12-10 22:00:13.697044 constructing the RangedSummarizedExperiment (rse) object. rowRanges(rse_gene_SRP009615_refseq) #> GRanges object with 54042 ranges and 25 metadata columns: #> seqnames ranges strand | source type bp_length @@ -685,17 +683,17 @@

    Examples

    proj_info, annotation = "ercc" ) -#> 2023-05-07 00:10:59.736376 downloading and reading the metadata. -#> 2023-05-07 00:11:00.02302 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:00.345005 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:00.66956 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:01.031001 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:01.36341 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:01.447554 downloading and reading the feature information. -#> 2023-05-07 00:11:01.718114 caching file human.gene_sums.ERCC.gtf.gz. -#> 2023-05-07 00:11:01.803771 downloading and reading the counts: 12 samples across 92 features. -#> 2023-05-07 00:11:02.067252 caching file sra.gene_sums.SRP009615.ERCC.gz. -#> 2023-05-07 00:11:02.17908 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:13.727693 downloading and reading the metadata. +#> 2024-12-10 22:00:14.13305 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:14.55116 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:15.085208 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:15.5358 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:15.984182 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:16.047669 downloading and reading the feature information. +#> 2024-12-10 22:00:16.46065 caching file human.gene_sums.ERCC.gtf.gz. +#> 2024-12-10 22:00:16.522762 downloading and reading the counts: 12 samples across 92 features. +#> 2024-12-10 22:00:16.883868 caching file sra.gene_sums.SRP009615.ERCC.gz. +#> 2024-12-10 22:00:17.0277 constructing the RangedSummarizedExperiment (rse) object. rowRanges(rse_gene_SRP009615_ercc) #> GRanges object with 92 ranges and 6 metadata columns: #> seqnames ranges strand | source type bp_length @@ -732,17 +730,17 @@

    Examples

    proj_info, annotation = "sirv" ) -#> 2023-05-07 00:11:02.211417 downloading and reading the metadata. -#> 2023-05-07 00:11:02.497324 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:02.886448 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:03.22362 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:03.557758 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:03.889899 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:03.989911 downloading and reading the feature information. -#> 2023-05-07 00:11:04.287838 caching file human.gene_sums.SIRV.gtf.gz. -#> 2023-05-07 00:11:04.387151 downloading and reading the counts: 12 samples across 7 features. -#> 2023-05-07 00:11:04.643488 caching file sra.gene_sums.SRP009615.SIRV.gz. -#> 2023-05-07 00:11:04.946357 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:17.054664 downloading and reading the metadata. +#> 2024-12-10 22:00:17.466237 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:18.117469 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:18.518585 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:18.951903 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:19.403709 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:19.464729 downloading and reading the feature information. +#> 2024-12-10 22:00:19.848982 caching file human.gene_sums.SIRV.gtf.gz. +#> 2024-12-10 22:00:19.909621 downloading and reading the counts: 12 samples across 7 features. +#> 2024-12-10 22:00:20.29934 caching file sra.gene_sums.SRP009615.SIRV.gz. +#> 2024-12-10 22:00:20.384122 constructing the RangedSummarizedExperiment (rse) object. rowRanges(rse_gene_SRP009615_sirv) #> GRanges object with 7 ranges and 5 metadata columns: #> seqnames ranges strand | source type bp_length @@ -770,72 +768,72 @@

    Examples

    rses_gene <- lapply(annotation_options(), function(x) { create_rse(proj_info, type = "gene", annotation = x) }) -#> 2023-05-07 00:11:04.97308 downloading and reading the metadata. -#> 2023-05-07 00:11:05.255507 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:05.573472 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:05.896726 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:06.22352 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:06.543992 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:06.627071 downloading and reading the feature information. -#> 2023-05-07 00:11:06.926447 caching file human.gene_sums.G026.gtf.gz. -#> 2023-05-07 00:11:07.418048 downloading and reading the counts: 12 samples across 63856 features. -#> 2023-05-07 00:11:07.680464 caching file sra.gene_sums.SRP009615.G026.gz. -#> 2023-05-07 00:11:07.860845 constructing the RangedSummarizedExperiment (rse) object. -#> 2023-05-07 00:11:07.883122 downloading and reading the metadata. -#> 2023-05-07 00:11:08.16528 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:08.493349 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:08.861712 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:09.19383 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:09.52885 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:09.628582 downloading and reading the feature information. -#> 2023-05-07 00:11:09.9042 caching file human.gene_sums.G029.gtf.gz. -#> 2023-05-07 00:11:10.480122 downloading and reading the counts: 12 samples across 64837 features. -#> 2023-05-07 00:11:10.747085 caching file sra.gene_sums.SRP009615.G029.gz. -#> 2023-05-07 00:11:10.916615 constructing the RangedSummarizedExperiment (rse) object. -#> 2023-05-07 00:11:10.938466 downloading and reading the metadata. -#> 2023-05-07 00:11:11.207739 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:11.582081 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:11.901201 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:12.224091 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:12.547452 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:12.632961 downloading and reading the feature information. -#> 2023-05-07 00:11:12.899991 caching file human.gene_sums.F006.gtf.gz. -#> 2023-05-07 00:11:13.338635 downloading and reading the counts: 12 samples across 124047 features. -#> 2023-05-07 00:11:13.593051 caching file sra.gene_sums.SRP009615.F006.gz. -#> 2023-05-07 00:11:13.889259 constructing the RangedSummarizedExperiment (rse) object. -#> 2023-05-07 00:11:13.911845 downloading and reading the metadata. -#> 2023-05-07 00:11:14.172178 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:14.515338 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:14.835939 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:15.157787 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:15.477671 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:15.559414 downloading and reading the feature information. -#> 2023-05-07 00:11:15.816875 caching file human.gene_sums.R109.gtf.gz. -#> 2023-05-07 00:11:16.457783 downloading and reading the counts: 12 samples across 54042 features. -#> 2023-05-07 00:11:16.690823 caching file sra.gene_sums.SRP009615.R109.gz. -#> 2023-05-07 00:11:17.646302 constructing the RangedSummarizedExperiment (rse) object. -#> 2023-05-07 00:11:17.669385 downloading and reading the metadata. -#> 2023-05-07 00:11:17.956727 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:18.259673 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:18.570068 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:18.891008 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:19.211854 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:19.293309 downloading and reading the feature information. -#> 2023-05-07 00:11:19.545496 caching file human.gene_sums.ERCC.gtf.gz. -#> 2023-05-07 00:11:19.628367 downloading and reading the counts: 12 samples across 92 features. -#> 2023-05-07 00:11:19.884436 caching file sra.gene_sums.SRP009615.ERCC.gz. -#> 2023-05-07 00:11:19.993551 constructing the RangedSummarizedExperiment (rse) object. -#> 2023-05-07 00:11:20.01458 downloading and reading the metadata. -#> 2023-05-07 00:11:20.29704 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:20.619707 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:20.955975 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:21.296625 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:21.632452 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:21.729379 downloading and reading the feature information. -#> 2023-05-07 00:11:21.986019 caching file human.gene_sums.SIRV.gtf.gz. -#> 2023-05-07 00:11:22.084423 downloading and reading the counts: 12 samples across 7 features. -#> 2023-05-07 00:11:22.335658 caching file sra.gene_sums.SRP009615.SIRV.gz. -#> 2023-05-07 00:11:22.462359 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:20.406306 downloading and reading the metadata. +#> 2024-12-10 22:00:20.8368 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:21.256897 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:21.695219 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:22.126059 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:22.574302 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:22.644475 downloading and reading the feature information. +#> 2024-12-10 22:00:23.035188 caching file human.gene_sums.G026.gtf.gz. +#> 2024-12-10 22:00:24.261491 downloading and reading the counts: 12 samples across 63856 features. +#> 2024-12-10 22:00:24.632636 caching file sra.gene_sums.SRP009615.G026.gz. +#> 2024-12-10 22:00:24.76039 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:24.778699 downloading and reading the metadata. +#> 2024-12-10 22:00:25.259591 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:25.677646 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:26.133257 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:26.571378 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:27.012645 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:27.074214 downloading and reading the feature information. +#> 2024-12-10 22:00:27.446333 caching file human.gene_sums.G029.gtf.gz. +#> 2024-12-10 22:00:27.797742 downloading and reading the counts: 12 samples across 64837 features. +#> 2024-12-10 22:00:28.187059 caching file sra.gene_sums.SRP009615.G029.gz. +#> 2024-12-10 22:00:28.327369 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:28.345621 downloading and reading the metadata. +#> 2024-12-10 22:00:28.754312 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:29.226323 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:29.701459 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:30.144257 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:30.617219 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:30.687863 downloading and reading the feature information. +#> 2024-12-10 22:00:31.076534 caching file human.gene_sums.F006.gtf.gz. +#> 2024-12-10 22:00:31.469819 downloading and reading the counts: 12 samples across 124047 features. +#> 2024-12-10 22:00:32.028316 caching file sra.gene_sums.SRP009615.F006.gz. +#> 2024-12-10 22:00:32.195657 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:32.214805 downloading and reading the metadata. +#> 2024-12-10 22:00:32.71148 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:33.133113 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:33.549713 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:34.03771 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:34.468951 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:34.530131 downloading and reading the feature information. +#> 2024-12-10 22:00:34.909121 caching file human.gene_sums.R109.gtf.gz. +#> 2024-12-10 22:00:35.317052 downloading and reading the counts: 12 samples across 54042 features. +#> 2024-12-10 22:00:35.720842 caching file sra.gene_sums.SRP009615.R109.gz. +#> 2024-12-10 22:00:35.922075 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:35.941285 downloading and reading the metadata. +#> 2024-12-10 22:00:36.349821 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:36.827126 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:37.239189 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:37.708132 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:38.111547 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:38.174953 downloading and reading the feature information. +#> 2024-12-10 22:00:38.528116 caching file human.gene_sums.ERCC.gtf.gz. +#> 2024-12-10 22:00:38.58879 downloading and reading the counts: 12 samples across 92 features. +#> 2024-12-10 22:00:38.962471 caching file sra.gene_sums.SRP009615.ERCC.gz. +#> 2024-12-10 22:00:39.05023 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:39.067776 downloading and reading the metadata. +#> 2024-12-10 22:00:39.538704 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:39.960842 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:40.393221 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:40.829023 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:41.26145 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:41.330419 downloading and reading the feature information. +#> 2024-12-10 22:00:41.724384 caching file human.gene_sums.SIRV.gtf.gz. +#> 2024-12-10 22:00:41.793921 downloading and reading the counts: 12 samples across 7 features. +#> 2024-12-10 22:00:42.217387 caching file sra.gene_sums.SRP009615.SIRV.gz. +#> 2024-12-10 22:00:42.313657 constructing the RangedSummarizedExperiment (rse) object. names(rses_gene) <- annotation_options() rses_gene #> $gencode_v26 @@ -913,17 +911,17 @@

    Examples

    proj_info, type = "exon" ) -#> 2023-05-07 00:11:22.566979 downloading and reading the metadata. -#> 2023-05-07 00:11:22.849387 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:23.19788 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:23.833256 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:24.190655 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:24.621315 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:24.734605 downloading and reading the feature information. -#> 2023-05-07 00:11:25.016062 caching file human.exon_sums.G026.gtf.gz. -#> 2023-05-07 00:11:46.831422 downloading and reading the counts: 12 samples across 1299686 features. -#> 2023-05-07 00:11:47.362236 caching file sra.exon_sums.SRP009615.G026.gz. -#> 2023-05-07 00:11:48.649303 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:00:42.381407 downloading and reading the metadata. +#> 2024-12-10 22:00:42.755326 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:00:43.215806 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:00:43.639803 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:44.090516 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:00:44.575561 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:00:44.658582 downloading and reading the feature information. +#> 2024-12-10 22:00:45.033765 caching file human.exon_sums.G026.gtf.gz. +#> 2024-12-10 22:01:02.959407 downloading and reading the counts: 12 samples across 1299686 features. +#> 2024-12-10 22:01:03.824915 caching file sra.exon_sums.SRP009615.G026.gz. +#> 2024-12-10 22:01:04.920433 constructing the RangedSummarizedExperiment (rse) object. ## Explore the resulting RSE exon object rse_exon_SRP009615 @@ -1069,19 +1067,19 @@

    Examples

    proj_info, type = "jxn" ) -#> 2023-05-07 00:11:52.826972 downloading and reading the metadata. -#> 2023-05-07 00:11:53.116512 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:11:53.423539 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:11:53.746409 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:54.072303 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:11:54.386513 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:11:54.471267 downloading and reading the feature information. -#> 2023-05-07 00:11:54.790385 caching file sra.junctions.SRP009615.ALL.RR.gz. -#> 2023-05-07 00:11:56.49752 downloading and reading the counts: 12 samples across 281448 features. -#> 2023-05-07 00:11:56.796275 caching file sra.junctions.SRP009615.ALL.MM.gz. -#> 2023-05-07 00:11:57.576621 matching exon-exon junction counts with the metadata. -#> 2023-05-07 00:11:57.838492 caching file sra.junctions.SRP009615.ALL.ID.gz. -#> 2023-05-07 00:11:57.941144 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:01:08.395473 downloading and reading the metadata. +#> 2024-12-10 22:01:08.882415 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:01:09.338097 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:01:09.744249 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:10.173463 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:10.614309 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:01:10.675857 downloading and reading the feature information. +#> 2024-12-10 22:01:11.070317 caching file sra.junctions.SRP009615.ALL.RR.gz. +#> 2024-12-10 22:01:12.800938 downloading and reading the counts: 12 samples across 281448 features. +#> 2024-12-10 22:01:13.301129 caching file sra.junctions.SRP009615.ALL.MM.gz. +#> 2024-12-10 22:01:13.871022 matching exon-exon junction counts with the metadata. +#> 2024-12-10 22:01:14.262616 caching file sra.junctions.SRP009615.ALL.ID.gz. +#> 2024-12-10 22:01:14.331726 constructing the RangedSummarizedExperiment (rse) object. ## Explore the resulting RSE exon-exon junctions object rse_jxn_SRP009615 @@ -1145,12 +1143,12 @@

    Examples

    #> 60.30 MB ## Obtain a list of RSE objects for all exon annotations -if (FALSE) { +if (FALSE) { # \dontrun{ rses_exon <- lapply(annotation_options(), function(x) { create_rse(proj_info, type = "exon", annotation = x, verbose = FALSE) }) names(rses_exon) <- annotation_options() -} +} # }
    @@ -1165,15 +1163,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/create_rse_manual.html b/reference/create_rse_manual.html index 8d827fd..b5618cf 100644 --- a/reference/create_rse_manual.html +++ b/reference/create_rse_manual.html @@ -1,12 +1,12 @@ -Internal function for creating a recount3 RangedSummarizedExperiment object — create_rse_manual • recount3Internal function for creating a recount3 RangedSummarizedExperiment object — create_rse_manual • recount3 - +
    @@ -31,7 +31,7 @@
    - +
    @@ -84,44 +84,46 @@

    Internal function for creating a recount3 RangedSummarizedExperiment object<

    Arguments

    -
    project
    + + +
    project

    A character(1) with the ID for a given study.

    -
    project_home
    +
    project_home

    A character(1) with the home directory for the project. You can find these using project_homes().

    -
    type
    +
    type

    A character(1) specifying whether you want to access gene, exon, or exon-exon junction counts.

    -
    organism
    +
    organism

    A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".

    -
    annotation
    +
    annotation

    A character(1) specifying which annotation you want to download. Only used when type is either gene or exon.

    -
    bfc
    +
    bfc

    A BiocFileCache-class object where the files will be cached to, typically created by recount3_cache().

    -
    jxn_format
    +
    jxn_format

    A character(1) specifying whether the exon-exon junction files are derived from all the reads (ALL) or only the uniquely mapping read counts (UNIQUE). Note that UNIQUE is only available for some projects: GTEx and TCGA for human.

    -
    recount3_url
    +
    recount3_url

    A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be @@ -132,20 +134,16 @@

    Arguments

    you have a favorite mirror.

    -
    verbose
    +
    verbose

    A logical(1) indicating whether to show messages with updates.

    Value

    - - -

    A -RangedSummarizedExperiment-class

    - - -

    object.

    +

    A +RangedSummarizedExperiment-class +object.

    References

    @@ -154,7 +152,7 @@

    References

    See also

    -

    Other internal functions for accessing the recount3 data: +

    Other internal functions for accessing the recount3 data: annotation_ext(), file_retrieve(), locate_url_ann(), @@ -173,17 +171,17 @@

    Examples

    "SRP009615", "data_sources/sra" ) -#> 2023-05-07 00:12:00.557621 downloading and reading the metadata. -#> 2023-05-07 00:12:00.848869 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:12:01.193886 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:12:01.510686 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:12:01.833772 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:12:02.15607 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:12:02.477324 downloading and reading the feature information. -#> 2023-05-07 00:12:02.745714 caching file human.gene_sums.G026.gtf.gz. -#> 2023-05-07 00:12:03.220237 downloading and reading the counts: 12 samples across 63856 features. -#> 2023-05-07 00:12:03.489067 caching file sra.gene_sums.SRP009615.G026.gz. -#> 2023-05-07 00:12:03.656085 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:01:15.956605 downloading and reading the metadata. +#> 2024-12-10 22:01:16.450202 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:01:16.843767 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:01:17.282748 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:17.718456 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:18.133807 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:01:18.194561 downloading and reading the feature information. +#> 2024-12-10 22:01:18.57243 caching file human.gene_sums.G026.gtf.gz. +#> 2024-12-10 22:01:18.939992 downloading and reading the counts: 12 samples across 63856 features. +#> 2024-12-10 22:01:19.316672 caching file sra.gene_sums.SRP009615.G026.gz. +#> 2024-12-10 22:01:20.721078 constructing the RangedSummarizedExperiment (rse) object. rse_gene_SRP009615_manual #> class: RangedSummarizedExperiment #> dim: 63856 12 @@ -208,19 +206,19 @@

    Examples

    "collections/geuvadis_smartseq", recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3" ) -#> 2023-05-07 00:12:03.785307 downloading and reading the metadata. -#> 2023-05-07 00:12:04.265943 caching file geuvadis_smartseq.recount_project.gz. -#> 2023-05-07 00:12:04.466651 caching file sra.sra.ERP110066.MD.gz. -#> 2023-05-07 00:12:04.657549 caching file sra.recount_project.ERP110066.MD.gz. -#> 2023-05-07 00:12:04.85334 caching file sra.recount_qc.ERP110066.MD.gz. +#> 2024-12-10 22:01:20.818954 downloading and reading the metadata. +#> 2024-12-10 22:01:21.366222 caching file geuvadis_smartseq.recount_project.gz. +#> 2024-12-10 22:01:21.566189 caching file sra.sra.ERP110066.MD.gz. +#> 2024-12-10 22:01:21.75569 caching file sra.recount_project.ERP110066.MD.gz. +#> 2024-12-10 22:01:21.94748 caching file sra.recount_qc.ERP110066.MD.gz. #> Warning: The 'url' <http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_seq_qc.ERP110066.MD.gz> does not exist or is not available. -#> 2023-05-07 00:12:05.179351 caching file sra.recount_pred.ERP110066.MD.gz. -#> 2023-05-07 00:12:05.378524 caching file geuvadis_smartseq.custom.gz. -#> 2023-05-07 00:12:05.648144 downloading and reading the feature information. -#> 2023-05-07 00:12:05.778548 caching file human.gene_sums.G026.gtf.gz. -#> 2023-05-07 00:12:06.283255 downloading and reading the counts: 1 sample across 63856 features. -#> 2023-05-07 00:12:06.413842 caching file sra.gene_sums.ERP110066.G026.gz. -#> 2023-05-07 00:12:08.762478 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:01:22.28931 caching file sra.recount_pred.ERP110066.MD.gz. +#> 2024-12-10 22:01:22.482653 caching file geuvadis_smartseq.custom.gz. +#> 2024-12-10 22:01:22.670555 downloading and reading the feature information. +#> 2024-12-10 22:01:22.818949 caching file human.gene_sums.G026.gtf.gz. +#> 2024-12-10 22:01:23.168626 downloading and reading the counts: 1 sample across 63856 features. +#> 2024-12-10 22:01:23.318131 caching file sra.gene_sums.ERP110066.G026.gz. +#> 2024-12-10 22:01:24.675643 constructing the RangedSummarizedExperiment (rse) object. rse_gene_ERP110066_collection_manual #> class: RangedSummarizedExperiment #> dim: 63856 1 @@ -243,17 +241,17 @@

    Examples

    "data_sources/sra", organism = "mouse" ) -#> 2023-05-07 00:12:08.888969 downloading and reading the metadata. -#> 2023-05-07 00:12:14.578888 caching file sra.sra.DRP002367.MD.gz. -#> 2023-05-07 00:12:14.93374 caching file sra.recount_project.DRP002367.MD.gz. -#> 2023-05-07 00:12:15.297514 caching file sra.recount_qc.DRP002367.MD.gz. -#> 2023-05-07 00:12:15.615882 caching file sra.recount_seq_qc.DRP002367.MD.gz. -#> 2023-05-07 00:12:15.936019 caching file sra.recount_pred.DRP002367.MD.gz. -#> 2023-05-07 00:12:16.016256 downloading and reading the feature information. -#> 2023-05-07 00:12:16.279003 caching file mouse.gene_sums.M023.gtf.gz. -#> 2023-05-07 00:12:18.000451 downloading and reading the counts: 4 samples across 55421 features. -#> 2023-05-07 00:12:18.284909 caching file sra.gene_sums.DRP002367.M023.gz. -#> 2023-05-07 00:12:18.411522 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:01:24.768728 downloading and reading the metadata. +#> 2024-12-10 22:01:25.562307 caching file sra.sra.DRP002367.MD.gz. +#> 2024-12-10 22:01:25.997055 caching file sra.recount_project.DRP002367.MD.gz. +#> 2024-12-10 22:01:26.438528 caching file sra.recount_qc.DRP002367.MD.gz. +#> 2024-12-10 22:01:26.885771 caching file sra.recount_seq_qc.DRP002367.MD.gz. +#> 2024-12-10 22:01:27.320311 caching file sra.recount_pred.DRP002367.MD.gz. +#> 2024-12-10 22:01:27.387908 downloading and reading the feature information. +#> 2024-12-10 22:01:27.768896 caching file mouse.gene_sums.M023.gtf.gz. +#> 2024-12-10 22:01:28.108315 downloading and reading the counts: 4 samples across 55421 features. +#> 2024-12-10 22:01:28.473004 caching file sra.gene_sums.DRP002367.M023.gz. +#> 2024-12-10 22:01:28.588882 constructing the RangedSummarizedExperiment (rse) object. rse_gene_DRP002367_manual #> class: RangedSummarizedExperiment #> dim: 55421 4 @@ -269,13 +267,13 @@

    Examples

    ## Information about how this RSE was made metadata(rse_gene_DRP002367_manual) #> $time_created -#> [1] "2023-05-07 00:12:18 UTC" +#> [1] "2024-12-10 22:01:28 UTC" #> #> $recount3_version #> package ondiskversion loadedversion path -#> recount3 recount3 1.11.2 1.11.2 /__w/_temp/Library/recount3 +#> recount3 recount3 1.17.0 1.17.0 /__w/_temp/Library/recount3 #> loadedpath attached is_base date source -#> recount3 /__w/_temp/Library/recount3 TRUE FALSE 2023-05-07 Bioconductor +#> recount3 /__w/_temp/Library/recount3 TRUE FALSE 2024-12-10 Bioconductor #> md5ok library #> recount3 NA /__w/_temp/Library #> @@ -300,7 +298,7 @@

    Examples

    ## Test with a collection that has one sample, at the exon level ## NOTE: this requires loading the full data for this study (nearly 6GB!) -if (FALSE) { +if (FALSE) { # \dontrun{ rse_exon_ERP110066_collection_manual <- create_rse_manual( "ERP110066", "collections/geuvadis_smartseq", @@ -327,9 +325,9 @@

    Examples

    ## Check how much memory this RSE object uses ## NOTE: this doesn't run since 2 files are missing on the test site! pryr::object_size(rse_jxn_ERP110066_collection_manual) -} +} # } -if (FALSE) { +if (FALSE) { # \dontrun{ ## For testing and debugging project <- "ERP110066" project_home <- "collections/geuvadis_smartseq" @@ -343,7 +341,7 @@

    Examples

    bfc <- recount3_cache() recount3_url <- "http://idies.jhu.edu/recount3/data" verbose <- TRUE -} +} # }
    @@ -358,15 +356,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/expand_sra_attributes.html b/reference/expand_sra_attributes.html index fa86f44..557fd85 100644 --- a/reference/expand_sra_attributes.html +++ b/reference/expand_sra_attributes.html @@ -1,12 +1,12 @@ -Expand SRA attributes — expand_sra_attributes • recount3Expand SRA attributes — expand_sra_attributes • recount3 - +
    @@ -31,7 +31,7 @@
    - +
    @@ -74,19 +74,17 @@

    Expand SRA attributes

    Arguments

    -
    rse
    + + +
    rse

    A RangedSummarizedExperiment-class object created by create_rse() or create_rse_manual().

    Value

    - - -

    A RangedSummarizedExperiment-class

    - - -

    object with expanded metadata columns.

    +

    A RangedSummarizedExperiment-class +object with expanded metadata columns.

    Details

    @@ -106,9 +104,9 @@

    Examples

    
     ## Find all available human projects
     human_projects <- available_projects()
    -#> 2023-05-07 00:12:18.971639 caching file sra.recount_project.MD.gz.
    -#> 2023-05-07 00:12:19.291246 caching file gtex.recount_project.MD.gz.
    -#> 2023-05-07 00:12:19.631356 caching file tcga.recount_project.MD.gz.
    +#> 2024-12-10 22:01:29.182618 caching file sra.recount_project.MD.gz.
    +#> 2024-12-10 22:01:29.614085 caching file gtex.recount_project.MD.gz.
    +#> 2024-12-10 22:01:30.035782 caching file tcga.recount_project.MD.gz.
     
     ## Find the project you are interested in
     proj_info <- subset(
    @@ -118,17 +116,17 @@ 

    Examples

    ## Create a RSE object at the gene level rse_gene_SRP009615 <- create_rse(proj_info) -#> 2023-05-07 00:12:21.845299 downloading and reading the metadata. -#> 2023-05-07 00:12:22.180084 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:12:22.496025 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:12:22.814289 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:12:23.151212 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:12:23.475999 caching file sra.recount_pred.SRP009615.MD.gz. -#> 2023-05-07 00:12:23.558369 downloading and reading the feature information. -#> 2023-05-07 00:12:23.841686 caching file human.gene_sums.G026.gtf.gz. -#> 2023-05-07 00:12:24.337531 downloading and reading the counts: 12 samples across 63856 features. -#> 2023-05-07 00:12:24.608303 caching file sra.gene_sums.SRP009615.G026.gz. -#> 2023-05-07 00:12:24.787148 constructing the RangedSummarizedExperiment (rse) object. +#> 2024-12-10 22:01:31.842301 downloading and reading the metadata. +#> 2024-12-10 22:01:32.25808 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:01:32.722892 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:01:33.154502 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:33.700977 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:34.149767 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:01:34.208994 downloading and reading the feature information. +#> 2024-12-10 22:01:34.642825 caching file human.gene_sums.G026.gtf.gz. +#> 2024-12-10 22:01:35.003811 downloading and reading the counts: 12 samples across 63856 features. +#> 2024-12-10 22:01:35.375571 caching file sra.gene_sums.SRP009615.G026.gz. +#> 2024-12-10 22:01:35.509445 constructing the RangedSummarizedExperiment (rse) object. ## Expand the SRA attributes (see details for more information) rse_gene_SRP009615 <- expand_sra_attributes(rse_gene_SRP009615) @@ -146,15 +144,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/file_retrieve.html b/reference/file_retrieve.html index 3f858a8..e6a15af 100644 --- a/reference/file_retrieve.html +++ b/reference/file_retrieve.html @@ -1,9 +1,9 @@ -Download a remote file and cache it to re-use later — file_retrieve • recount3Download a remote file and cache it to re-use later — file_retrieve • recount3 - +
    @@ -28,7 +28,7 @@
    - +
    @@ -72,32 +72,32 @@

    Download a remote file and cache it to re-use later

    Arguments

    -
    url
    + + +
    url

    A character(1) with the file URL or the actual local path in which case, it won't be cached. If length(url) > 1 , this function will be used recursively.

    -
    bfc
    +
    bfc

    A BiocFileCache-class object where the files will be cached to, typically created by recount3_cache().

    -
    verbose
    +
    verbose

    A logical(1) indicating whether to show messages with updates.

    Value

    - - -

    A character(1) with the path to the cached file.

    +

    A character(1) with the path to the cached file.

    See also

    -

    Other internal functions for accessing the recount3 data: +

    Other internal functions for accessing the recount3 data: annotation_ext(), create_rse_manual(), locate_url_ann(), @@ -118,22 +118,22 @@

    Examples

    local_SRP009615_meta <- file_retrieve( url = url_SRP009615_meta ) -#> 2023-05-07 00:12:25.437357 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:12:25.749973 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:12:26.070817 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:12:26.409835 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:12:26.724754 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:01:36.08779 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:01:36.542605 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:01:36.995848 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:37.433981 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:37.858852 caching file sra.recount_pred.SRP009615.MD.gz. local_SRP009615_meta #> sra.sra.SRP009615.MD.gz -#> "/github/home/.cache/R/recount3/22486fd6f29d_sra.sra.SRP009615.MD.gz" +#> "/github/home/.cache/R/recount3/227e18ae2f4c_sra.sra.SRP009615.MD.gz" #> sra.recount_project.SRP009615.MD.gz -#> "/github/home/.cache/R/recount3/2248613da13d_sra.recount_project.SRP009615.MD.gz" +#> "/github/home/.cache/R/recount3/227e18d97a94_sra.recount_project.SRP009615.MD.gz" #> sra.recount_qc.SRP009615.MD.gz -#> "/github/home/.cache/R/recount3/2248638ef0e5_sra.recount_qc.SRP009615.MD.gz" +#> "/github/home/.cache/R/recount3/227e42553808_sra.recount_qc.SRP009615.MD.gz" #> sra.recount_seq_qc.SRP009615.MD.gz -#> "/github/home/.cache/R/recount3/2248157b9e27_sra.recount_seq_qc.SRP009615.MD.gz" +#> "/github/home/.cache/R/recount3/227e474eb65b_sra.recount_seq_qc.SRP009615.MD.gz" #> sra.recount_pred.SRP009615.MD.gz -#> "/github/home/.cache/R/recount3/22487841d23_sra.recount_pred.SRP009615.MD.gz" +#> "/github/home/.cache/R/recount3/227e57a81614_sra.recount_pred.SRP009615.MD.gz" ## Download the gene counts file for project SRP009615 url_SRP009615_gene <- locate_url( @@ -144,10 +144,10 @@

    Examples

    local_SRP009615_gene <- file_retrieve( url = url_SRP009615_gene ) -#> 2023-05-07 00:12:27.071847 caching file sra.gene_sums.SRP009615.G026.gz. +#> 2024-12-10 22:01:38.311329 caching file sra.gene_sums.SRP009615.G026.gz. local_SRP009615_gene -#> sra.gene_sums.SRP009615.G026.gz -#> "/github/home/.cache/R/recount3/224837bbd78_sra.gene_sums.SRP009615.G026.gz" +#> sra.gene_sums.SRP009615.G026.gz +#> "/github/home/.cache/R/recount3/227e2ae5d501_sra.gene_sums.SRP009615.G026.gz"
    @@ -162,15 +162,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/index.html b/reference/index.html index 8592571..265aad3 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,9 +1,9 @@ -Function reference • recount3Package index • recount3 - +
    @@ -28,7 +28,7 @@
    - +
    @@ -157,15 +157,15 @@

    All functions
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/is_paired_end.html b/reference/is_paired_end.html index 860d93f..dbc6fa6 100644 --- a/reference/is_paired_end.html +++ b/reference/is_paired_end.html @@ -1,10 +1,10 @@ -Guess whether the samples are paired end — is_paired_end • recount3Guess whether the samples are paired end — is_paired_end • recount3 - +
    @@ -29,7 +29,7 @@
    - +
    @@ -74,34 +74,34 @@

    Guess whether the samples are paired end

    Arguments

    -
    x
    + + +
    x

    Either a RangedSummarizedExperiment-class created by create_rse() or the sample metadata created by read_metadata().

    -
    avg_mapped_read_length
    +
    avg_mapped_read_length

    A character(1) specifying the metdata column name that contains the average fragment length after aligning. This is typically twice the average read length for paired-end reads.

    -
    avg_read_length
    +
    avg_read_length

    A character(1) specifying the metadata column name that contains the average read length prior to aligning.

    Value

    - - -

    A logical() vector specifying whether each sample was likely +

    A logical() vector specifying whether each sample was likely paired-end or not.

    See also

    -

    Other count transformation functions: +

    Other count transformation functions: compute_read_counts(), compute_scale_factors(), transform_counts()

    @@ -119,11 +119,11 @@

    Examples

    ) ) ) -#> 2023-05-07 00:12:27.585102 caching file sra.sra.SRP009615.MD.gz. -#> 2023-05-07 00:12:27.907695 caching file sra.recount_project.SRP009615.MD.gz. -#> 2023-05-07 00:12:28.24191 caching file sra.recount_qc.SRP009615.MD.gz. -#> 2023-05-07 00:12:28.579797 caching file sra.recount_seq_qc.SRP009615.MD.gz. -#> 2023-05-07 00:12:28.912438 caching file sra.recount_pred.SRP009615.MD.gz. +#> 2024-12-10 22:01:38.898621 caching file sra.sra.SRP009615.MD.gz. +#> 2024-12-10 22:01:39.363913 caching file sra.recount_project.SRP009615.MD.gz. +#> 2024-12-10 22:01:39.959124 caching file sra.recount_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:40.346302 caching file sra.recount_seq_qc.SRP009615.MD.gz. +#> 2024-12-10 22:01:40.79932 caching file sra.recount_pred.SRP009615.MD.gz. ## Are the samples paired end? is_paired_end(SRP009615_meta) @@ -141,11 +141,11 @@

    Examples

    ) ) ) -#> 2023-05-07 00:12:29.291998 caching file sra.sra.DRP000499.MD.gz. -#> 2023-05-07 00:12:29.636309 caching file sra.recount_project.DRP000499.MD.gz. -#> 2023-05-07 00:12:29.984132 caching file sra.recount_qc.DRP000499.MD.gz. -#> 2023-05-07 00:12:30.343642 caching file sra.recount_seq_qc.DRP000499.MD.gz. -#> 2023-05-07 00:12:30.707121 caching file sra.recount_pred.DRP000499.MD.gz. +#> 2024-12-10 22:01:41.233278 caching file sra.sra.DRP000499.MD.gz. +#> 2024-12-10 22:01:41.64884 caching file sra.recount_project.DRP000499.MD.gz. +#> 2024-12-10 22:01:42.106257 caching file sra.recount_qc.DRP000499.MD.gz. +#> 2024-12-10 22:01:42.540452 caching file sra.recount_seq_qc.DRP000499.MD.gz. +#> 2024-12-10 22:01:42.988749 caching file sra.recount_pred.DRP000499.MD.gz. is_paired_end(DRP000499_meta) #> Warning: is_paired_end(): Looks like some samples failed to align and will return NA. #> DRR001622 DRR001623 DRR001624 DRR001625 DRR001626 DRR001627 DRR001628 DRR001629 @@ -168,15 +168,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/locate_url.html b/reference/locate_url.html index 36d05fd..76a3669 100644 --- a/reference/locate_url.html +++ b/reference/locate_url.html @@ -1,11 +1,11 @@ -Construct the URL to access a particular recount3 file — locate_url • recount3Construct the URL to access a particular recount3 file — locate_url • recount3 - +
    @@ -30,7 +30,7 @@
    - +
    @@ -81,44 +81,46 @@

    Construct the URL to access a particular recount3 file

    Arguments

    -
    project
    + + +
    project

    A character(1) with the ID for a given study.

    -
    project_home
    +
    project_home

    A character(1) with the home directory for the project. You can find these using project_homes().

    -
    type
    +
    type

    A character(1) specifying whether you want to access gene counts, exon counts, exon-exon junctions or base-pair BigWig coverage files (one per sample).

    -
    organism
    +
    organism

    A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".

    -
    sample
    +
    sample

    A character() vector with the sample ID(s) you want to download.

    -
    annotation
    +
    annotation

    A character(1) specifying which annotation you want to download. Only used when type is either gene or exon.

    -
    jxn_format
    +
    jxn_format

    A character(1) specifying whether the exon-exon junction files are derived from all the reads (ALL) or only the uniquely mapping read counts (UNIQUE). Note that UNIQUE is only available for some projects: GTEx and TCGA for human.

    -
    recount3_url
    +
    recount3_url

    A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be @@ -131,13 +133,11 @@

    Arguments

    Value

    - - -

    A character() with the URL(s) for the file(s) of interest.

    +

    A character() with the URL(s) for the file(s) of interest.

    See also

    -

    Other internal functions for accessing the recount3 data: +

    Other internal functions for accessing the recount3 data: annotation_ext(), create_rse_manual(), file_retrieve(), @@ -172,7 +172,7 @@

    Examples

    "collections/geuvadis_smartseq", recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3" ) -#> 2023-05-07 00:12:31.505758 caching file geuvadis_smartseq.recount_project.gz. +#> 2024-12-10 22:01:43.585023 caching file geuvadis_smartseq.recount_project.gz. #> sra.sra.ERP110066.MD.gz #> "http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.sra.ERP110066.MD.gz" #> sra.recount_project.ERP110066.MD.gz @@ -221,7 +221,7 @@

    Examples

    "gene", recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3" ) -#> 2023-05-07 00:12:31.703993 caching file geuvadis_smartseq.recount_project.gz. +#> 2024-12-10 22:01:43.797593 caching file geuvadis_smartseq.recount_project.gz. #> sra.gene_sums.ERP110066.G026.gz #> "http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/gene_sums/66/ERP110066/sra.gene_sums.ERP110066.G026.gz" @@ -267,15 +267,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/locate_url_ann.html b/reference/locate_url_ann.html index 4aae477..4f6cb96 100644 --- a/reference/locate_url_ann.html +++ b/reference/locate_url_ann.html @@ -1,11 +1,11 @@ -Construct the URL to a recount3 annotation file — locate_url_ann • recount3Construct the URL to a recount3 annotation file — locate_url_ann • recount3 - +
    @@ -30,7 +30,7 @@
    - +
    @@ -77,22 +77,24 @@

    Construct the URL to a recount3 annotation file

    Arguments

    -
    type
    + + +
    type

    A character(1) specifying whether you want to access gene counts or exon data.

    -
    organism
    +
    organism

    A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".

    -
    annotation
    +
    annotation

    A character(1) specifying which annotation you want to download. Only used when type is either gene or exon.

    -
    recount3_url
    +
    recount3_url

    A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be @@ -105,14 +107,12 @@

    Arguments

    Value

    - - -

    A character(1) with the URL (or file path) to access the +

    A character(1) with the URL (or file path) to access the recount3 annotation file.

    See also

    -

    Other internal functions for accessing the recount3 data: +

    Other internal functions for accessing the recount3 data: annotation_ext(), create_rse_manual(), file_retrieve(), @@ -145,15 +145,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/project_homes.html b/reference/project_homes.html index 68e6255..4e16b45 100644 --- a/reference/project_homes.html +++ b/reference/project_homes.html @@ -1,10 +1,10 @@ -Find available project home options — project_homes • recount3Find available project home options — project_homes • recount3 - +
    @@ -29,7 +29,7 @@
    - +
    @@ -73,12 +73,14 @@

    Find available project home options

    Arguments

    -
    organism
    + + +
    organism

    A character(1) specifying which organism you want to download data from. Supported options are "human" or "mouse".

    -
    recount3_url
    +
    recount3_url

    A character(1) specifying the home URL for recount3 or a local directory where you have mirrored recount3. Defaults to the load balancer http://duffel.rail.bio/recount3, but can also be @@ -91,9 +93,7 @@

    Arguments

    Value

    - - -

    A character() vector with the available project_home options.

    +

    A character() vector with the available project_home options.

    Details

    @@ -104,7 +104,7 @@

    Details

    See also

    -

    Other internal functions for accessing the recount3 data: +

    Other internal functions for accessing the recount3 data: annotation_ext(), create_rse_manual(), file_retrieve(), @@ -145,15 +145,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/read_counts.html b/reference/read_counts.html index 7d24d8f..44c02c0 100644 --- a/reference/read_counts.html +++ b/reference/read_counts.html @@ -1,11 +1,11 @@ -Read a counts file — read_counts • recount3Read a counts file — read_counts • recount3 - +
    @@ -30,7 +30,7 @@
    - +
    @@ -72,12 +72,14 @@

    Read a counts file

    Arguments

    -
    counts_file
    + + +
    counts_file

    A character(1) with the local path to a recount3 counts file.

    -
    samples
    +
    samples

    A character() with external_id sample IDs to read in. When NULL (default), all samples will be read in. This argument is used by create_rse_manual().

    @@ -85,9 +87,7 @@

    Arguments

    Value

    - - -

    A data.frame() with sample IDs as the column names.

    +

    A data.frame() with sample IDs as the column names.

    References

    @@ -96,7 +96,7 @@

    References

    See also

    -

    Other internal functions for accessing the recount3 data: +

    Other internal functions for accessing the recount3 data: annotation_ext(), create_rse_manual(), file_retrieve(), @@ -116,12 +116,12 @@

    Examples

    type = "gene" ) local_SRP009615_gene <- file_retrieve(url = url_SRP009615_gene) -#> 2023-05-07 00:12:32.972618 caching file sra.gene_sums.SRP009615.G026.gz. +#> 2024-12-10 22:01:44.998174 caching file sra.gene_sums.SRP009615.G026.gz. ## Read the gene counts, take about 3 seconds system.time(SRP009615_gene_counts <- read_counts(local_SRP009615_gene)) #> user system elapsed -#> 0.103 0.004 0.106 +#> 0.072 0.012 0.083 dim(SRP009615_gene_counts) #> [1] 63856 12 @@ -168,10 +168,10 @@

    Examples

    type = "exon" ) ) -#> 2023-05-07 00:12:34.394238 caching file sra.exon_sums.SRP009615.G026.gz. +#> 2024-12-10 22:01:46.496267 caching file sra.exon_sums.SRP009615.G026.gz. local_SRP009615_exon #> sra.exon_sums.SRP009615.G026.gz -#> "/github/home/.cache/R/recount3/2248fa92647_sra.exon_sums.SRP009615.G026.gz" +#> "/github/home/.cache/R/recount3/227e3dc2494_sra.exon_sums.SRP009615.G026.gz" ## Read the exon counts, takes about 50-60 seconds system.time( @@ -180,7 +180,7 @@

    Examples

    ) ) #> user system elapsed -#> 0.929 0.104 1.033 +#> 0.825 0.120 0.946 dim(SRP009615_exon_counts) #> [1] 1299686 12 pryr::object_size(SRP009615_exon_counts) @@ -233,15 +233,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/read_metadata.html b/reference/read_metadata.html index 34e8269..49765ca 100644 --- a/reference/read_metadata.html +++ b/reference/read_metadata.html @@ -1,11 +1,11 @@ -Read the metadata files — read_metadata • recount3Read the metadata files — read_metadata • recount3 - +
    @@ -30,7 +30,7 @@
    - +
    @@ -72,21 +72,21 @@

    Read the metadata files

    Arguments

    -
    metadata_files
    + + +
    metadata_files

    A character() with the local path to recount3 metadata files.

    Value

    - - -

    A data.frame() with all lower case column names for the sample +

    A data.frame() with all lower case column names for the sample metadata.

    See also

    -

    Other internal functions for accessing the recount3 data: +

    Other internal functions for accessing the recount3 data: annotation_ext(), create_rse_manual(), file_retrieve(), @@ -107,11 +107,11 @@

    Examples

    local_ERP110066_meta <- file_retrieve( url = url_ERP110066_meta ) -#> 2023-05-07 00:12:41.356664 caching file sra.sra.ERP110066.MD.gz. -#> 2023-05-07 00:12:41.680826 caching file sra.recount_project.ERP110066.MD.gz. -#> 2023-05-07 00:12:42.002532 caching file sra.recount_qc.ERP110066.MD.gz. -#> 2023-05-07 00:12:42.338177 caching file sra.recount_seq_qc.ERP110066.MD.gz. -#> 2023-05-07 00:12:42.665478 caching file sra.recount_pred.ERP110066.MD.gz. +#> 2024-12-10 22:01:52.052806 caching file sra.sra.ERP110066.MD.gz. +#> 2024-12-10 22:01:52.43945 caching file sra.recount_project.ERP110066.MD.gz. +#> 2024-12-10 22:01:52.852546 caching file sra.recount_qc.ERP110066.MD.gz. +#> 2024-12-10 22:01:53.273989 caching file sra.recount_seq_qc.ERP110066.MD.gz. +#> 2024-12-10 22:01:53.696044 caching file sra.recount_pred.ERP110066.MD.gz. ## Read the metadata ERP110066_meta <- read_metadata(local_ERP110066_meta) @@ -305,13 +305,13 @@

    Examples

    ) ) ) -#> 2023-05-07 00:12:43.328535 caching file geuvadis_smartseq.recount_project.gz. -#> 2023-05-07 00:12:43.531988 caching file sra.sra.ERP110066.MD.gz. -#> 2023-05-07 00:12:43.724762 caching file sra.recount_project.ERP110066.MD.gz. -#> 2023-05-07 00:12:43.920917 caching file sra.recount_qc.ERP110066.MD.gz. +#> 2024-12-10 22:01:54.403719 caching file geuvadis_smartseq.recount_project.gz. +#> 2024-12-10 22:01:54.602726 caching file sra.sra.ERP110066.MD.gz. +#> 2024-12-10 22:01:54.791541 caching file sra.recount_project.ERP110066.MD.gz. +#> 2024-12-10 22:01:54.982425 caching file sra.recount_qc.ERP110066.MD.gz. #> Warning: The 'url' <http://snaptron.cs.jhu.edu/data/temp/recount3/human/data_sources/sra/metadata/66/ERP110066/sra.recount_seq_qc.ERP110066.MD.gz> does not exist or is not available. -#> 2023-05-07 00:12:44.247336 caching file sra.recount_pred.ERP110066.MD.gz. -#> 2023-05-07 00:12:44.448955 caching file geuvadis_smartseq.custom.gz. +#> 2024-12-10 22:01:55.324019 caching file sra.recount_pred.ERP110066.MD.gz. +#> 2024-12-10 22:01:55.51829 caching file geuvadis_smartseq.custom.gz. dim(ERP110066_collection_meta) #> [1] 1 161 ## New columns for this collection @@ -324,11 +324,11 @@

    Examples

    locate_url("DRP002367", "data_sources/sra", organism = "mouse") ) ) -#> 2023-05-07 00:12:45.597233 caching file sra.sra.DRP002367.MD.gz. -#> 2023-05-07 00:12:46.163738 caching file sra.recount_project.DRP002367.MD.gz. -#> 2023-05-07 00:12:46.506557 caching file sra.recount_qc.DRP002367.MD.gz. -#> 2023-05-07 00:12:47.069095 caching file sra.recount_seq_qc.DRP002367.MD.gz. -#> 2023-05-07 00:12:47.62098 caching file sra.recount_pred.DRP002367.MD.gz. +#> 2024-12-10 22:01:56.316369 caching file sra.sra.DRP002367.MD.gz. +#> 2024-12-10 22:01:56.739578 caching file sra.recount_project.DRP002367.MD.gz. +#> 2024-12-10 22:01:57.150314 caching file sra.recount_qc.DRP002367.MD.gz. +#> 2024-12-10 22:01:57.617343 caching file sra.recount_seq_qc.DRP002367.MD.gz. +#> 2024-12-10 22:01:58.090484 caching file sra.recount_pred.DRP002367.MD.gz. dim(DRP002367_meta) #> [1] 4 176 @@ -338,10 +338,10 @@

    Examples

    locate_url("BLADDER", "data_sources/gtex") ) ) -#> 2023-05-07 00:12:48.21889 caching file gtex.gtex.BLADDER.MD.gz. -#> 2023-05-07 00:12:48.850269 caching file gtex.recount_project.BLADDER.MD.gz. -#> 2023-05-07 00:12:49.43457 caching file gtex.recount_qc.BLADDER.MD.gz. -#> 2023-05-07 00:12:50.005816 caching file gtex.recount_seq_qc.BLADDER.MD.gz. +#> 2024-12-10 22:01:58.558149 caching file gtex.gtex.BLADDER.MD.gz. +#> 2024-12-10 22:01:59.007259 caching file gtex.recount_project.BLADDER.MD.gz. +#> 2024-12-10 22:01:59.429224 caching file gtex.recount_qc.BLADDER.MD.gz. +#> 2024-12-10 22:01:59.877645 caching file gtex.recount_seq_qc.BLADDER.MD.gz. dim(gtex_bladder_meta) #> [1] 21 197 @@ -557,15 +557,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/recount3-package.html b/reference/recount3-package.html index 649434d..0ff6664 100644 --- a/reference/recount3-package.html +++ b/reference/recount3-package.html @@ -1,10 +1,10 @@ -recount3: Explore and download data from the recount3 project — recount3-package • recount3recount3: Explore and download data from the recount3 project — recount3-package • recount3 - +
    @@ -29,7 +29,7 @@
    - +
    @@ -88,15 +88,15 @@

    Author

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/recount3_cache.html b/reference/recount3_cache.html index 116adf1..7fb277b 100644 --- a/reference/recount3_cache.html +++ b/reference/recount3_cache.html @@ -1,11 +1,11 @@ -Specify where to cache the recount3 files — recount3_cache • recount3Specify where to cache the recount3 files — recount3_cache • recount3 - +
    @@ -30,7 +30,7 @@
    - +
    @@ -72,23 +72,21 @@

    Specify where to cache the recount3 files

    Arguments

    -
    cache_dir
    + + +
    cache_dir

    A character(1) specifying the directory that will be used for caching the data. If NULL a sensible default location will be used.

    Value

    - - -

    A BiocFileCache-class

    - - -

    object where the recount3 files will be cached to.

    +

    A BiocFileCache-class +object where the recount3 files will be cached to.

    See also

    -

    Other recount3 cache functions: +

    Other recount3 cache functions: recount3_cache_files(), recount3_cache_rm()

    @@ -116,15 +114,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/recount3_cache_files.html b/reference/recount3_cache_files.html index c4a05d4..f85ed83 100644 --- a/reference/recount3_cache_files.html +++ b/reference/recount3_cache_files.html @@ -1,10 +1,10 @@ -Locate recount3 cached files — recount3_cache_files • recount3Locate recount3 cached files — recount3_cache_files • recount3 - +
    @@ -29,7 +29,7 @@
    - +
    @@ -70,7 +70,9 @@

    Locate recount3 cached files

    Arguments

    -
    bfc
    + + +
    bfc

    A BiocFileCache-class object where the files will be cached to, typically created by recount3_cache().

    @@ -78,14 +80,12 @@

    Arguments

    Value

    - - -

    A character() with the URLs of the recount3 files you have +

    A character() with the URLs of the recount3 files you have downloaded.

    See also

    -

    Other recount3 cache functions: +

    Other recount3 cache functions: recount3_cache_rm(), recount3_cache()

    @@ -169,15 +169,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/recount3_cache_rm.html b/reference/recount3_cache_rm.html index 3c5ffd4..081230f 100644 --- a/reference/recount3_cache_rm.html +++ b/reference/recount3_cache_rm.html @@ -1,10 +1,10 @@ -Remove recount3 cached files — recount3_cache_rm • recount3Remove recount3 cached files — recount3_cache_rm • recount3 - +
    @@ -29,7 +29,7 @@
    - +
    @@ -70,7 +70,9 @@

    Remove recount3 cached files

    Arguments

    -
    bfc
    + + +
    bfc

    A BiocFileCache-class object where the files will be cached to, typically created by recount3_cache().

    @@ -78,13 +80,11 @@

    Arguments

    Value

    - - -

    A character(0) if the removal of files was successful.

    +

    A character(0) if the removal of files was successful.

    See also

    -

    Other recount3 cache functions: +

    Other recount3 cache functions: recount3_cache_files(), recount3_cache()

    @@ -154,13 +154,13 @@

    Examples

    #> [59] "http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/67/SRP103067/sra.recount_qc.SRP103067.MD.gz" #> [60] "http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/67/SRP103067/sra.recount_seq_qc.SRP103067.MD.gz" #> [61] "http://duffel.rail.bio/recount3/human/data_sources/sra/metadata/67/SRP103067/sra.recount_pred.SRP103067.MD.gz" -if (FALSE) { +if (FALSE) { # \dontrun{ ## Now delete the cached files recount3_cache_rm() ## List againt your recount3 files (should be empty) recount3_cache_files() -} +} # }
    @@ -175,15 +175,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

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transform_counts • recount3 - +
    @@ -39,7 +39,7 @@
    - +
    @@ -97,13 +97,15 @@

    Transform the raw counts provided by the recount3 project

    Arguments

    -
    rse
    + + +
    rse

    A RangedSummarizedExperiment-class created by create_rse().

    -
    by
    +
    by

    Either auc or mapped_reads. If set to auc it will compute the scaling factor by the total coverage of the sample. That is, the area under the curve (AUC) of the coverage. If set to mapped_reads it @@ -111,31 +113,29 @@

    Arguments

    whether the library was paired-end or not, and the desired read length (L).

    -
    targetSize
    +
    targetSize

    A numeric(1) specifying the target library size in number of single end reads.

    -
    L
    +
    L

    A integer(1) specifying the target read length. It is only used when by = 'mapped_reads' since it cancels out in the calculation when using by = 'auc'.

    -
    round
    +
    round

    A logical(1) specifying whether to round the transformed counts or not.

    -
    ...
    +
    ...

    Further arguments passed to compute_scale_factors().

    Value

    - - -

    A matrix() with the transformed (scaled) counts.

    +

    A matrix() with the transformed (scaled) counts.

    Details

    @@ -145,7 +145,7 @@

    Details

    See also

    -

    Other count transformation functions: +

    Other count transformation functions: compute_read_counts(), compute_scale_factors(), is_paired_end()

    @@ -156,17 +156,17 @@

    Examples

    
     ## Create a RSE object at the gene level
     rse_gene_SRP009615 <- create_rse_manual("SRP009615")
    -#> 2023-05-07 00:12:51.616844 downloading and reading the metadata.
    -#> 2023-05-07 00:12:52.103045 caching file sra.sra.SRP009615.MD.gz.
    -#> 2023-05-07 00:12:52.699716 caching file sra.recount_project.SRP009615.MD.gz.
    -#> 2023-05-07 00:12:53.047657 caching file sra.recount_qc.SRP009615.MD.gz.
    -#> 2023-05-07 00:12:53.58639 caching file sra.recount_seq_qc.SRP009615.MD.gz.
    -#> 2023-05-07 00:12:54.127138 caching file sra.recount_pred.SRP009615.MD.gz.
    -#> 2023-05-07 00:12:54.213777 downloading and reading the feature information.
    -#> 2023-05-07 00:12:54.685976 caching file human.gene_sums.G026.gtf.gz.
    -#> 2023-05-07 00:12:55.198254 downloading and reading the counts: 12 samples across 63856 features.
    -#> 2023-05-07 00:12:55.680187 caching file sra.gene_sums.SRP009615.G026.gz.
    -#> 2023-05-07 00:12:55.865277 constructing the RangedSummarizedExperiment (rse) object.
    +#> 2024-12-10 22:02:01.249605 downloading and reading the metadata.
    +#> 2024-12-10 22:02:01.664448 caching file sra.sra.SRP009615.MD.gz.
    +#> 2024-12-10 22:02:02.100315 caching file sra.recount_project.SRP009615.MD.gz.
    +#> 2024-12-10 22:02:02.52262 caching file sra.recount_qc.SRP009615.MD.gz.
    +#> 2024-12-10 22:02:02.971792 caching file sra.recount_seq_qc.SRP009615.MD.gz.
    +#> 2024-12-10 22:02:03.428006 caching file sra.recount_pred.SRP009615.MD.gz.
    +#> 2024-12-10 22:02:03.48893 downloading and reading the feature information.
    +#> 2024-12-10 22:02:03.88364 caching file human.gene_sums.G026.gtf.gz.
    +#> 2024-12-10 22:02:04.250031 downloading and reading the counts: 12 samples across 63856 features.
    +#> 2024-12-10 22:02:04.64963 caching file sra.gene_sums.SRP009615.G026.gz.
    +#> 2024-12-10 22:02:04.785268 constructing the RangedSummarizedExperiment (rse) object.
     
     ## Scale the counts using the AUC
     assays(rse_gene_SRP009615)$counts <- transform_counts(rse_gene_SRP009615)
    @@ -233,15 +233,15 @@ 

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

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