diff --git a/404.html b/404.html index 6001a55..cce2562 100644 --- a/404.html +++ b/404.html @@ -6,7 +6,7 @@ Page not found (404) • GenomicState - + @@ -19,7 +19,7 @@ - +
@@ -53,7 +53,7 @@
  • - +
    • @@ -64,7 +64,7 @@
    - +
    @@ -92,16 +92,16 @@

    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 c389e05..7df720e 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -1,9 +1,9 @@ -Contributor Covenant Code of Conduct • GenomicStateContributor Covenant Code of Conduct • GenomicState - +
    @@ -34,14 +34,14 @@
    - +
    @@ -132,15 +132,15 @@

    Attribution -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 2597ed4..d1dcbd7 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -1,9 +1,9 @@ -Contributing to GenomicState • GenomicStateContributing to GenomicState • GenomicState - +
    @@ -34,14 +34,14 @@
    - +
    @@ -95,15 +95,15 @@

    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 9f84ba0..71f55a0 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -1,9 +1,9 @@ -Getting help with GenomicState • GenomicStateGetting help with GenomicState • GenomicState - +
    @@ -34,14 +34,14 @@
    - +
    @@ -93,15 +93,15 @@

    What happens next? -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/GenomicState.html b/articles/GenomicState.html index 03f85ec..4495870 100644 --- a/articles/GenomicState.html +++ b/articles/GenomicState.html @@ -6,21 +6,20 @@ Introduction to GenomicState • GenomicState - + - - +
    @@ -54,7 +53,7 @@
  • - +
    • @@ -65,7 +64,7 @@
    - +
    @@ -79,9 +78,9 @@

    Leonardo University
    -

    7 May 2023

    +

    12 December 2024

    - Source: vignettes/GenomicState.Rmd + Source: vignettes/GenomicState.Rmd
    @@ -92,39 +91,39 @@

    7 May 2023

    Basics

    -

    Install GenomicState +

    Install GenomicState

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

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

    Required knowledge

    -

    GenomicState +

    GenomicState is based on many other packages and in particular in those that have implemented the infrastructure needed for dealing with annotation data. -That is, packages like rtracklayer -that allow you to import the data. A GenomicState +That is, packages like rtracklayer +that allow you to import the data. A GenomicState user is not expected to deal with those packages directly but will need -to be familiar with derfinder -and derfinderPlot -to understand the results GenomicState +to be familiar with derfinder +and derfinderPlot +to understand the results GenomicState generates. Furthermore, it’ll be useful for the user to know the syntax -of AnnotationHub -(Morgan and Shepherd, 2023) in order to query and load the data provided +of AnnotationHub +(Morgan and Shepherd, 2024) in order to query and load the data provided by this package.

    If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this @@ -147,9 +146,9 @@

    Asking for help

    -

    Citing GenomicState +

    Citing GenomicState

    -

    We hope that GenomicState +

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

    @@ -157,21 +156,21 @@ 
    Citing citation("GenomicState")
 #> To cite package 'GenomicState' in publications use:
 #> 
-#>   Collado-Torres L (2023). _Build and access GenomicState objects for
+#>   Collado-Torres L (2024). _Build and access GenomicState objects for
 #>   use with derfinder tools from sources like Gencode_.
 #>   doi:10.18129/B9.bioc.GenomicState
 #>   <https://doi.org/10.18129/B9.bioc.GenomicState>,
 #>   https://github.com/LieberInstitute/GenomicState - R package version
-#>   0.99.15, <http://www.bioconductor.org/packages/GenomicState>.
+#>   0.99.16, <http://www.bioconductor.org/packages/GenomicState>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
 #>     title = {Build and access GenomicState objects for use with derfinder tools from sources like Gencode},
 #>     author = {Leonardo Collado-Torres},
-#>     year = {2023},
+#>     year = {2024},
 #>     url = {http://www.bioconductor.org/packages/GenomicState},
-#>     note = {https://github.com/LieberInstitute/GenomicState - R package version 0.99.15},
+#>     note = {https://github.com/LieberInstitute/GenomicState - R package version 0.99.16},
 #>     doi = {10.18129/B9.bioc.GenomicState},
 #>   }
    @@ -179,10 +178,10 @@

    Citing

    Overview

    -

    The GenomicState +

    The GenomicState package was developed for speeding up analyses that require these objects and in particular those that rely on Gencode annotation data. -The package GenomicState +The package GenomicState provides functions for building GenomicState objects from diverse annotation sources such as Gencode. It also provides a way to load pre-computed GenomicState @@ -190,7 +189,7 @@

    Overviewderfinder::makeGenomicState() and can be used for annotating regions with derfinder::annotateRegions() which are in turn used by derfinderPlot::plotRegionCoverage().

    -

    To get started, load the GenomicState +

    To get started, load the GenomicState package.

    @@ -199,9 +198,9 @@

    OverviewAnnotationHub

    Using the GencodeStateHub() function you can query and -download the data from GenomicState -using AnnotationHub -(Morgan and Shepherd, 2023).

    +download the data from GenomicState +using AnnotationHub +(Morgan and Shepherd, 2024).

     ## Query AnnotationHub for the GenomicState object for Gencode v31 on
 ## hg19 coordinates
@@ -212,7 +211,7 @@ 
    AnnotationHub)
 hub_query_gs_gencode_v31_hg19
 #> AnnotationHub with 1 record
-#> # snapshotDate(): 2023-04-06
+#> # snapshotDate(): 2024-10-28
 #> # names(): AH75184
 #> # $dataprovider: GENCODE
 #> # $species: Homo sapiens
@@ -252,19 +251,6 @@ 
    AnnotationHubhub_gs_gencode_v31_hg19
 }
 #> loading from cache
-#> Loading required package: GenomicRanges
-#> Loading required package: stats4
-#> Loading required package: S4Vectors
-#> 
-#> Attaching package: 'S4Vectors'
-#> The following object is masked from 'package:utils':
-#> 
-#>     findMatches
-#> The following objects are masked from 'package:base':
-#> 
-#>     expand.grid, I, unname
-#> Loading required package: IRanges
-#> Loading required package: GenomeInfoDb
 #> $fullGenome
 #> GRanges object with 659263 ranges and 5 metadata columns:
 #>          seqnames            ranges strand |   theRegion         tx_id
@@ -343,6 +329,19 @@ 
    Using the objects)
 )
 #> Loading required package: GenomicFeatures
+#> Loading required package: S4Vectors
+#> Loading required package: stats4
+#> 
+#> Attaching package: 'S4Vectors'
+#> The following object is masked from 'package:utils':
+#> 
+#>     findMatches
+#> The following objects are masked from 'package:base':
+#> 
+#>     expand.grid, I, unname
+#> Loading required package: IRanges
+#> Loading required package: GenomeInfoDb
+#> Loading required package: GenomicRanges
 #> Loading required package: AnnotationDbi
 #> Loading required package: Biobase
 #> Welcome to Bioconductor
@@ -358,7 +357,7 @@ 
    Using the objects## Build the GenomicState and annotated genes
 genes_v31_hg19_chr21 <- gencode_annotated_genes(txdb_v31_hg19_chr21)
-#> 2023-05-07 06:38:40.521147 annotating the transcripts
+#> 2024-12-12 22:30:33.505134 annotating the transcripts
 #> No annotationPackage supplied. Trying org.Hs.eg.db.
 #> Loading required package: org.Hs.eg.db
 #> 
@@ -368,14 +367,14 @@ 
    Using the objects#> Annotating genes.
 #> 'select()' returned 1:many mapping between keys and columns
 gs_v31_hg19_chr21 <- gencode_genomic_state(txdb_v31_hg19_chr21)
-#> 2023-05-07 06:39:02.822717 making the GenomicState object
+#> 2024-12-12 22:30:55.884377 making the GenomicState object
 #> extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
 #> 'select()' returned 1:1 mapping between keys and columns
-#> 2023-05-07 06:39:10.73445 finding gene symbols
+#> 2024-12-12 22:31:01.676907 finding gene symbols
 #> 'select()' returned 1:many mapping between keys and columns
-#> 2023-05-07 06:39:11.121002 adding gene symbols to the GenomicState
    -

    You can alternatively use the files hosted in AnnotationHub -(Morgan and Shepherd, 2023) which will be faster in general.

    +#> 2024-12-12 22:31:01.958252 adding gene symbols to the GenomicState +

    You can alternatively use the files hosted in AnnotationHub +(Morgan and Shepherd, 2024) which will be faster in general.

    Next we load a series of related packages that use the objects we -created with GenomicState -or downloaded from AnnotationHub -(Morgan and Shepherd, 2023).

    +created with GenomicState +or downloaded from AnnotationHub +(Morgan and Shepherd, 2024).

    Next we can prepare the needed for running derfinderPlot::plotRegionCoverage() where we use the @@ -494,14 +493,14 @@

    Using the objects= regions, genomicState = gs_v31_hg19_chr21$fullGenome, minoverlap = 1 ) -#> 2023-05-07 06:39:25.058838 annotateRegions: counting -#> 2023-05-07 06:39:25.141558 annotateRegions: annotating +#> 2024-12-12 22:31:12.075855 annotateRegions: counting +#> 2024-12-12 22:31:12.135269 annotateRegions: annotating ## Obtain fullCov object fullCov <- list("chr21" = genomeDataRaw$coverage) regionCov <- getRegionCoverage(fullCov = fullCov, regions = regions) -#> 2023-05-07 06:39:25.275779 getRegionCoverage: processing chr21 -#> 2023-05-07 06:39:25.329103 getRegionCoverage: done processing chr21 +#> 2024-12-12 22:31:12.230014 getRegionCoverage: processing chr21 +#> 2024-12-12 22:31:12.268195 getRegionCoverage: done processing chr21

    And now we can make the example plot as shown below.

     ## now make the plot
@@ -542,8 +541,8 @@ 
    JHPCE
 
    
 
    Build objects
 
    
-
    The objects provided by GenomicState through AnnotationHub
-(Morgan and Shepherd, 2023) were built using code like the one included
+
    The objects provided by GenomicState through AnnotationHub
+(Morgan and Shepherd, 2024) were built using code like the one included
 below which is how the Gencode version 23 for hg19 files were built.
    
 
     outdir <- "gencode"
@@ -586,15 +585,15 @@ 
    Build objects
 
    Reproducibility
 
    
-
    The GenomicState
-package (Collado-Torres, 2023) was made possible thanks to:
    
+
    The GenomicState
+package (Collado-Torres, 2024) was made possible thanks to:
    
 
 
    Code for creating the vignette
    
 
    @@ -658,184 +660,182 @@ 
    Reproducibilitylibrary("knitr")
 knit("GenomicState.Rmd", tangle = TRUE)
    
 
    Date the vignette was generated.
    
-
    #> [1] "2023-05-07 06:39:26 UTC"
    
+
    #> [1] "2024-12-12 22:31:13 UTC"
    
 
    Wallclock time spent generating the vignette.
    
-
    #> Time difference of 1.135 mins
    
+
    #> Time difference of 59.052 secs
    
 
    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     2024-12-12
+#>  pandoc   3.5 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
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 #> 
 #>  [1] /__w/_temp/Library
 #>  [2] /usr/local/lib/R/site-library
@@ -846,16 +846,16 @@ 
    Reproducibility
 
    Bibliography
 
    
-
    This vignette was generated using BiocStyle
-(Oleś, 2023), knitr (Xie,
+
    This vignette was generated using BiocStyle
+(Oleś, 2024), knitr (Xie,
 2014) and rmarkdown
-(Allaire, Xie, Dervieux et al., 2023) running behind the scenes.
    
+(Allaire, Xie, Dervieux et al., 2024) running behind the scenes.
    
 
    Citations made with RefManageR
 (McLean, 2017).
    
 
    
-[1]
+[1]
 J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents
-for R. R package version 2.21. 2023. URL:
+for R. R package version 2.29. 2024. URL:
 https://github.com/rstudio/rmarkdown.
 
    
 
    
@@ -865,24 +865,24 @@ 
    Bibliography10.18129/B9.bioc.GenomeInfoDb.
 
    
 
    
-[3]
+[3]
 Bioconductor Package Maintainer. AnnotationHubData: Transform public
 data resources into Bioconductor Data Structures. R package version
-1.30.0. 2023. DOI:
+1.36.0. 2024. DOI:
 10.18129/B9.bioc.AnnotationHubData.
 URL:
 https://bioconductor.org/packages/AnnotationHubData.
 
    
 
    
-[4]
+[4]
 M. Carlson. org.Hs.eg.db: Genome wide annotation for Human. R
-package version 3.17.0. 2023.
+package version 3.20.0. 2024.
 
    
 
    
-[5]
+[5]
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 with derfinder tools from sources like Gencode. https://github.com/LieberInstitute/GenomicState - R
-package version 0.99.15. 2023. DOI:
+package version 0.99.16. 2024. DOI:
 10.18129/B9.bioc.GenomicState.
 URL:
 http://www.bioconductor.org/packages/GenomicState.
@@ -897,8 +897,10 @@ 
    Bibliographyhttp://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852.
 
    
 
    
-[7]
-J. Hester and J. Bryan. glue: Interpreted String Literals. https://github.com/tidyverse/glue, https://glue.tidyverse.org/. 2022.
+[7]
+J. Hester and J. Bryan. glue: Interpreted String Literals. R
+package version 1.8.0, https://github.com/tidyverse/glue. 2024. URL:
+https://glue.tidyverse.org/.
 
    
 
    
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@@ -936,50 +938,60 @@ 
    Bibliography10.21105/joss.00338.
 
    
 
    
-[12]
+[12]
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-AnnotationHub resources. R package version 3.8.0. 2023. DOI:
+AnnotationHub resources. R package version 3.14.0. 2024. DOI:
 10.18129/B9.bioc.AnnotationHub.
 URL:
 https://bioconductor.org/packages/AnnotationHub.
 
    
 
    
-[13]
+[13]
 A. Oleś. BiocStyle: Standard styles for vignettes and other
-Bioconductor documents. R package version 2.28.0. 2023. DOI:
+Bioconductor documents. R package version 2.34.0. 2024. DOI:
 10.18129/B9.bioc.BiocStyle.
 URL:
 https://bioconductor.org/packages/BiocStyle.
 
    
 
    
-[14]
+[14]
+H. Pagès, M. Carlson, P. Aboyoun, et al. txdbmaker: Tools for making
+TxDb objects from genomic annotations. R package version 1.2.1.
+2024. DOI:
+10.18129/B9.bioc.txdbmaker.
+URL:
+https://bioconductor.org/packages/txdbmaker.
+
    
+
    
+[15]
 H. Pagès, M. Carlson, S. Falcon, et al. AnnotationDbi: Manipulation
 of SQLite-based annotations in Bioconductor. R package version
-1.62.1. 2023. DOI:
+1.68.0. 2024. DOI:
 10.18129/B9.bioc.AnnotationDbi.
 URL:
 https://bioconductor.org/packages/AnnotationDbi.
 
    
 
    
-[15]
+[16]
 R Core Team. R: A Language and Environment for Statistical
 Computing. R Foundation for Statistical Computing. Vienna, Austria,
-2023. URL:
+2024. URL:
 https://www.R-project.org/.
 
    
 
    
-[16]
+[17]
 H. Wickham. “testthat: Get Started with Testing”. In: The R
 Journal 3 (2011), pp. 5–10. URL:
 https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf.
 
    
 
    
-[17]
+[18]
 H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session
-Information. https://github.com/r-lib/sessioninfo#readme, https://r-lib.github.io/sessioninfo/. 2021.
+Information. R package version 1.2.2, https://r-lib.github.io/sessioninfo/. 2021. URL:
+https://github.com/r-lib/sessioninfo#readme.
 
    
 
    
-[18]
+[19]
 Y. Xie. “knitr: A Comprehensive Tool for Reproducible Research in R”.
 In: Implementing Reproducible Computational Research. Ed. by V.
 Stodden, F. Leisch and R. D. Peng. ISBN 978-1466561595. Chapman and
@@ -990,9 +1002,7 @@ 
    Bibliography
 
-        
-
    
+
    @@ -1005,16 +1015,16 @@

    Bibliography

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/articles/GenomicState_files/figure-html/example_plot-1.png b/articles/GenomicState_files/figure-html/example_plot-1.png index 982e18b..df4f2ae 100644 Binary files a/articles/GenomicState_files/figure-html/example_plot-1.png and b/articles/GenomicState_files/figure-html/example_plot-1.png differ diff --git a/articles/GenomicState_files/figure-html/example_plot-2.png b/articles/GenomicState_files/figure-html/example_plot-2.png index 28fcc1c..f136b89 100644 Binary files a/articles/GenomicState_files/figure-html/example_plot-2.png and b/articles/GenomicState_files/figure-html/example_plot-2.png differ diff --git a/articles/index.html b/articles/index.html index a08bdd2..c1526d0 100644 --- a/articles/index.html +++ b/articles/index.html @@ -1,9 +1,9 @@ -Articles • GenomicStateArticles • GenomicState - +
    @@ -34,14 +34,14 @@
    - +
    @@ -65,15 +65,15 @@

    All vignettes

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/authors.html b/authors.html index 9fa10c0..ffab100 100644 --- a/authors.html +++ b/authors.html @@ -1,9 +1,9 @@ -Authors and Citation • GenomicStateAuthors and Citation • GenomicState - +
    @@ -34,23 +34,23 @@
    - +
    -

    Authors

    +

    Authors and Citation

    - +

    • Leonardo Collado-Torres. Author, maintainer.

      @@ -59,21 +59,21 @@

      Authors

      Citation

      - Source: inst/CITATION + Source: inst/CITATION
      -

      Collado-Torres L (2023). +

      Collado-Torres L (2024). Build and access GenomicState objects for use with derfinder tools from sources like Gencode. -doi:10.18129/B9.bioc.GenomicState, https://github.com/LieberInstitute/GenomicState - R package version 0.99.15, http://www.bioconductor.org/packages/GenomicState. +doi:10.18129/B9.bioc.GenomicState, https://github.com/LieberInstitute/GenomicState - R package version 0.99.16, http://www.bioconductor.org/packages/GenomicState. 

      @Manual{,
   title = {Build and access GenomicState objects for use with derfinder tools from sources like Gencode},
   author = {Leonardo Collado-Torres},
-  year = {2023},
+  year = {2024},
   url = {http://www.bioconductor.org/packages/GenomicState},
-  note = {https://github.com/LieberInstitute/GenomicState - R package version 0.99.15},
+  note = {https://github.com/LieberInstitute/GenomicState - R package version 0.99.16},
   doi = {10.18129/B9.bioc.GenomicState},
 }
      @@ -88,15 +88,15 @@

      Citation

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/index.html b/index.html index 07a37ae..b1929ba 100644 --- a/index.html +++ b/index.html @@ -5,26 +5,22 @@ -Build and access GenomicState objects for use with derfinder tools from - sources like Gencode • GenomicState - +Build and access GenomicState objects for use with derfinder tools from sources like Gencode • GenomicState + - - + + - +
    @@ -58,7 +54,7 @@
  • - +
    • @@ -69,7 +65,7 @@
    - +
    @@ -93,7 +89,7 @@

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

    +BiocManager::install("GenomicState")

    Citation @@ -190,7 +186,7 @@

    Dev status

  • Bioc downloads rank
  • Bioc support
  • Codecov test coverage
    • -
  • R build status
    • +
  • R build status
  • GitHub issues
  • GitHub pulls
    • @@ -207,16 +203,16 @@

    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 5c5586b..367b125 100644 --- a/news/index.html +++ b/news/index.html @@ -1,9 +1,9 @@ -Changelog • GenomicStateChangelog • GenomicState - +
    @@ -34,20 +34,20 @@
    - +

    Changelog

    - Source: NEWS.md + Source: NEWS.md
    @@ -99,15 +99,15 @@

    GenomicSta

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/pkgdown.yml b/pkgdown.yml index f79a470..3406a19 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: GenomicState: GenomicState.html -last_built: 2023-05-07T06:37Z - +last_built: 2024-12-12T22:29Z diff --git a/reference/GenomicState-package.html b/reference/GenomicState-package.html index 29e0e22..b86c9cb 100644 --- a/reference/GenomicState-package.html +++ b/reference/GenomicState-package.html @@ -1,9 +1,9 @@ -GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode — GenomicState-package • GenomicStateGenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode — GenomicState-package • GenomicState - +
    @@ -34,20 +34,20 @@
    - +

    GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode

    - Source: R/GenomicState-package.R + Source: R/GenomicState-package.R
    @@ -79,15 +79,15 @@

    Author

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/GenomicStateHub.html b/reference/GenomicStateHub.html index 94e2b48..d48217a 100644 --- a/reference/GenomicStateHub.html +++ b/reference/GenomicStateHub.html @@ -1,12 +1,12 @@ -Access GenomicState objects through AnnotationHub — GenomicStateHub • GenomicStateAccess GenomicState objects through AnnotationHub — GenomicStateHub • GenomicState - +
    @@ -37,20 +37,20 @@
    - +

    Access GenomicState objects through AnnotationHub

    - Source: R/GenomicStateHub.R + Source: R/GenomicStateHub.R
    @@ -72,30 +72,30 @@

    Access GenomicState objects through AnnotationHub

    Arguments

    -
    version
    + + +
    version

    A character(1) with the Gencode version number.

    -
    genome
    +
    genome

    A character(1) with the human genome version number. Valid options are 'hg38' or 'hg19'.

    -
    filetype
    +
    filetype

    A character() with either TxDb, AnnotatedGenes or GenomicState.

    -
    ah
    +
    ah

    An AnnotationHub object AnnotationHub-class.

    Value

    - - -

    The AnnotationHub-class query +

    The AnnotationHub-class query for the file you requested.

    @@ -120,7 +120,7 @@

    Examples

    ) hub_query_gs_gencode_v31_hg19 #> AnnotationHub with 1 record -#> # snapshotDate(): 2023-04-06 +#> # snapshotDate(): 2024-10-28 #> # names(): AH75184 #> # $dataprovider: GENCODE #> # $species: Homo sapiens @@ -160,19 +160,6 @@

    Examples

    hub_gs_gencode_v31_hg19 } #> loading from cache -#> Loading required package: GenomicRanges -#> Loading required package: stats4 -#> Loading required package: S4Vectors -#> -#> Attaching package: ‘S4Vectors’ -#> The following object is masked from ‘package:utils’: -#> -#> findMatches -#> The following objects are masked from ‘package:base’: -#> -#> I, expand.grid, unname -#> Loading required package: IRanges -#> Loading required package: GenomeInfoDb #> $fullGenome #> GRanges object with 659263 ranges and 5 metadata columns: #> seqnames ranges strand | theRegion tx_id @@ -249,15 +236,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/gencode_annotated_genes.html b/reference/gencode_annotated_genes.html index a7b4c41..4509f96 100644 --- a/reference/gencode_annotated_genes.html +++ b/reference/gencode_annotated_genes.html @@ -1,11 +1,11 @@ -Annotation the genes for a given Gencode TxDb object — gencode_annotated_genes • GenomicStateAnnotation the genes for a given Gencode TxDb object — gencode_annotated_genes • GenomicState - +
    @@ -36,20 +36,20 @@
    - +

    Annotation the genes for a given Gencode TxDb object

    - Source: R/gencode_annotated_genes.R + Source: R/gencode_annotated_genes.R
    @@ -65,16 +65,16 @@

    Annotation the genes for a given Gencode TxDb object

    Arguments

    -
    txdb
    + + +
    txdb

    A GenomicFeatures::TxDb object built with gencode_txdb().

    Value

    - - -

    The annotated genes resulting from +

    The annotated genes resulting from bumphunter::annotateTranscripts().

    @@ -95,9 +95,9 @@

    Author

    Examples

    
 ## Start from scratch if you want:
-if (FALSE) {
+if (FALSE) { # \dontrun{
 txdb_v31_hg19_chr21 <- gencode_txdb("31", "hg19", chrs = "chr21")
-}
+} # }
 
 ## or read in the txdb object for hg19 chr21 from this package
 txdb_v31_hg19_chr21 <- AnnotationDbi::loadDb(
@@ -106,6 +106,19 @@ 
    Examples
    
     )
 )
 #> Loading required package: GenomicFeatures
+#> Loading required package: S4Vectors
+#> Loading required package: stats4
+#> 
+#> Attaching package: ‘S4Vectors’
+#> The following object is masked from ‘package:utils’:
+#> 
+#>     findMatches
+#> The following objects are masked from ‘package:base’:
+#> 
+#>     I, expand.grid, unname
+#> Loading required package: IRanges
+#> Loading required package: GenomeInfoDb
+#> Loading required package: GenomicRanges
 #> Loading required package: AnnotationDbi
 #> Loading required package: Biobase
 #> Welcome to Bioconductor
@@ -121,7 +134,7 @@ 
    Examples
    
 
 ## Obtain the annotated genes for the Gencode TxDb object
 genes_v31_hg19_chr21 <- gencode_annotated_genes(txdb_v31_hg19_chr21)
-#> 2023-05-07 06:37:45.658967 annotating the transcripts
+#> 2024-12-12 22:29:43.929076 annotating the transcripts
 #> No annotationPackage supplied. Trying org.Hs.eg.db.
 #> Loading required package: org.Hs.eg.db
 #> 
@@ -202,15 +215,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/gencode_genomic_state.html b/reference/gencode_genomic_state.html index 6f5ea2c..23fe2e8 100644 --- a/reference/gencode_genomic_state.html +++ b/reference/gencode_genomic_state.html @@ -1,12 +1,12 @@ -Build a GenomicState object for Gencode TxDb objects — gencode_genomic_state • GenomicStateBuild a GenomicState object for Gencode TxDb objects — gencode_genomic_state • GenomicState - +
    @@ -37,20 +37,20 @@
    - +

    Build a GenomicState object for Gencode TxDb objects

    - Source: R/gencode_genomic_state.R + Source: R/gencode_genomic_state.R
    @@ -67,16 +67,16 @@

    Build a GenomicState object for Gencode TxDb objects

    Arguments

    -
    txdb
    + + +
    txdb

    A GenomicFeatures::TxDb object built with gencode_txdb().

    Value

    - - -

    A GenomicState object with the gene symbols as built using +

    A GenomicState object with the gene symbols as built using derfinder::makeGenomicState().

    @@ -101,9 +101,9 @@

    Author

    Examples

    
 ## Start from scratch if you want:
-if (FALSE) {
+if (FALSE) { # \dontrun{
 txdb_v31_hg19_chr21 <- gencode_txdb("31", "hg19", chrs = "chr21")
-}
+} # }
 
 ## or read in the txdb object for hg19 chr21 from this package
 txdb_v31_hg19_chr21 <- AnnotationDbi::loadDb(
@@ -114,12 +114,12 @@ 
    Examples
    
 
 ## Now build the GenomicState object
 gs_v31_hg19_chr21 <- gencode_genomic_state(txdb_v31_hg19_chr21)
-#> 2023-05-07 06:38:09.080103 making the GenomicState object
+#> 2024-12-12 22:30:07.115845 making the GenomicState object
 #> extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
 #> 'select()' returned 1:1 mapping between keys and columns
-#> 2023-05-07 06:38:14.614311 finding gene symbols
+#> 2024-12-12 22:30:11.277921 finding gene symbols
 #> 'select()' returned 1:many mapping between keys and columns
-#> 2023-05-07 06:38:14.989506 adding gene symbols to the GenomicState
+#> 2024-12-12 22:30:11.605075 adding gene symbols to the GenomicState
 
 ## Explore the result
 gs_v31_hg19_chr21
@@ -199,15 +199,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/gencode_txdb.html b/reference/gencode_txdb.html index 623628f..bbf15a8 100644 --- a/reference/gencode_txdb.html +++ b/reference/gencode_txdb.html @@ -1,12 +1,12 @@ -Create a Gencode TxDb object — gencode_txdb • GenomicStateCreate a Gencode TxDb object — gencode_txdb • GenomicState - +
    @@ -37,20 +37,20 @@
    - +

    Create a Gencode TxDb object

    - Source: R/gencode_txdb.R + Source: R/gencode_txdb.R
    @@ -73,27 +73,25 @@

    Create a Gencode TxDb object

    Arguments

    -
    version
    + + +
    version

    A character(1) with the Gencode version number.

    -
    genome
    +
    genome

    A character(1) with the human genome version number. Valid options are 'hg38' or 'hg19'.

    -
    chrs
    +
    chrs

    A character() vector with the chromosome (contig) names to keep.

    Value

    - - -

    A GenomicFeatures::TxDb object.

    - - +

    A GenomicFeatures::TxDb object.

    A character(1) with the URL for the GTF Gencode file of interest.

    @@ -114,9 +112,9 @@

    Author

    Examples

    
 ## Start from scratch if you want:
-if (FALSE) {
+if (FALSE) { # \dontrun{
 txdb_v31_hg19_chr21 <- gencode_txdb("31", "hg19", chrs = "chr21")
-}
+} # }
 
 ## or read in the txdb object for hg19 chr21 from this package
 txdb_v31_hg19_chr21 <- AnnotationDbi::loadDb(
@@ -161,15 +159,15 @@ 
    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 c23a3e0..29a3ce5 100644 --- a/reference/index.html +++ b/reference/index.html @@ -1,9 +1,9 @@ -Function reference • GenomicStatePackage index • GenomicState - +
    @@ -34,14 +34,14 @@
    - +
    @@ -86,15 +86,15 @@

    All functions
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/reference/local_metadata.html b/reference/local_metadata.html index 9b53d48..b220f90 100644 --- a/reference/local_metadata.html +++ b/reference/local_metadata.html @@ -1,9 +1,9 @@ -Locate local metadata outside of AnnotationHub — local_metadata • GenomicStateLocate local metadata outside of AnnotationHub — local_metadata • GenomicState - +
    @@ -34,20 +34,20 @@
    - +

    Locate local metadata outside of AnnotationHub

    - Source: R/local_metadata.R + Source: R/local_metadata.R
    @@ -61,16 +61,16 @@

    Locate local metadata outside of AnnotationHub

    Arguments

    -
    local_path
    + + +
    local_path

    A character(1) pointing to where the data is stored locally

    Value

    - - -

    The AnnotationHub metadata data.frame() for the data in this +

    The AnnotationHub metadata data.frame() for the data in this package with RDataPath updated to point to the local_path. It includes an addtional column called loadCode which you can evaluate with eval(parse(text = entry)).

    @@ -136,15 +136,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/sitemap.xml b/sitemap.xml index 9c3d986..d5de94b 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,51 +1,19 @@ - - - - /404.html - - - /CODE_OF_CONDUCT.html - - - /CONTRIBUTING.html - - - /SUPPORT.html - - - /articles/GenomicState.html - - - /articles/index.html - - - /authors.html - - - /index.html - - - /news/index.html - - - /reference/GenomicState-package.html - - - /reference/GenomicStateHub.html - - - /reference/gencode_annotated_genes.html - - - /reference/gencode_genomic_state.html - - - /reference/gencode_txdb.html - - - /reference/index.html - - - /reference/local_metadata.html - + +/404.html +/CODE_OF_CONDUCT.html +/CONTRIBUTING.html +/SUPPORT.html +/articles/GenomicState.html +/articles/index.html +/authors.html +/index.html +/news/index.html +/reference/GenomicState-package.html +/reference/GenomicStateHub.html +/reference/gencode_annotated_genes.html +/reference/gencode_genomic_state.html +/reference/gencode_txdb.html +/reference/index.html +/reference/local_metadata.html +