qsvaR

LieberInstitute · Nov 30, 2021 · 4ea1e82 · 4ea1e82 · lcolladotor · Nov 30, 2021
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,4 +1,4 @@
-^DeDHeD\.Rproj$
+^qsvaR\.Rproj$
 ^\.Rproj\.user$
 ^dev$
 ^README\.Rmd$

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1,6 +1,6 @@
-# Contributing to DeDHeD
+# Contributing to qsvaR
 
-This outlines how to propose a change to DeDHeD. 
+This outlines how to propose a change to qsvaR. 
 For more detailed info about contributing to this, and other tidyverse packages, please see the
 [**development contributing guide**](https://rstd.io/tidy-contrib). 
 
@@ -18,7 +18,7 @@ If you’ve found a bug, please file an issue that illustrates the bug with a mi
 
 ### Pull request process
 
-*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("LieberInstitute/DeDHed", fork = TRUE)`.
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("LieberInstitute/qsvaR", fork = TRUE)`.
 
 *   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
     If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
@@ -42,6 +42,6 @@ If you’ve found a bug, please file an issue that illustrates the bug with a mi
 
 ## Code of Conduct
 
-Please note that the DeDHeD project is released with a
+Please note that the qsvaR project is released with a
 [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
 project you agree to abide by its terms.
diff --git a/.github/SUPPORT.md b/.github/SUPPORT.md
@@ -1,6 +1,6 @@
-# Getting help with `DeDHeD`
+# Getting help with `qsvaR`
 
-Thanks for using `DeDHeD`!
+Thanks for using `qsvaR`!
 Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.
 
 ## Make a reprex
@@ -14,14 +14,14 @@ For additional reprex pointers, check out the [Get help!](https://www.tidyverse.
 
 Armed with your reprex, the next step is to figure out [where to ask](https://www.tidyverse.org/help/#where-to-ask). See also the [Bioconductor help](http://bioconductor.org/help/) website.
 
-*   If it's a question: start with [community.rstudio.com](https://community.rstudio.com/), and/or StackOverflow. If this a Bioconductor-related question, please ask it at the [Bioconductor Support Website](https://support.bioconductor.org/) using the [appropriate package tag](https://support.bioconductor.org/t/DeDHeD) (the website will send an automatic email to the package authors). There are more people there to answer questions.
+*   If it's a question: start with [community.rstudio.com](https://community.rstudio.com/), and/or StackOverflow. If this a Bioconductor-related question, please ask it at the [Bioconductor Support Website](https://support.bioconductor.org/) using the [appropriate package tag](https://support.bioconductor.org/t/qsvaR) (the website will send an automatic email to the package authors). There are more people there to answer questions.
 
-*   If it's a bug: you're in the right place, [file an issue](https://github.com/LieberInstitute/DeDHed/issues/new).
+*   If it's a bug: you're in the right place, [file an issue](https://github.com/LieberInstitute/qsvaR/issues/new).
 
 *   If you're not sure: let the community help you figure it out!
     If your problem _is_ a bug or a feature request, you can easily return here and report it.
 
-Before opening a new issue, be sure to [search issues and pull requests](https://github.com/LieberInstitute/DeDHed/issues) to make sure the bug hasn't been reported and/or already fixed in the development version.
+Before opening a new issue, be sure to [search issues and pull requests](https://github.com/LieberInstitute/qsvaR/issues) to make sure the bug hasn't been reported and/or already fixed in the development version.
 By default, the search will be pre-populated with `is:issue is:open`.
 You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/)  (e.g. `is:pr`, `is:closed`) as needed.
 For example, you'd simply remove `is:open` to search _all_ issues in the repo, open or closed.

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -274,7 +274,7 @@ jobs:
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: lieberinstitute/dedhed
+          repository: lieberinstitute/qsvaR
           tag_with_ref: true
           tag_with_sha: true
           tags: latest
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,14 @@
-Package: DeDHeD
+Package: qsvaR
 Title: Generate Quality Surrogate Variable Analysis for Degradation Correction
 Version: 0.99.0
 Date: 2021-10-26
 Authors@R: 
     person("Joshua", "Stolz", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5694-5247"))
-Description: The DeDHeD package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.
+Description: The qsvaR package contains functions for removing the effect of degration in rna-seq data from postmortem brain tissue. The package is equipped to help users generate principal components associated with degradation. The components can be used in differential expression analysis to remove the effects of degradation.
 License: Artistic-2.0
-URL: https://github.com/LieberInstitute/DeDHed
-BugReports: https://support.bioconductor.org/t/DeDHeD
+URL: https://github.com/LieberInstitute/qsvaR
+BugReports: https://support.bioconductor.org/t/qsvaR
 biocViews: Software BiologicalQuestion DifferentialExpression WorkflowStep QualityControl
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# DeDHeD 0.99.0
+# qsvaR 0.99.0
 
 NEW FEATURES
 

diff --git a/README.Rmd b/README.Rmd
@@ -13,38 +13,38 @@ knitr::opts_chunk$set(
 )
 ```
 
-# DeDHeD
+# qsvaR
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/DeDHeD.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/DeDHeD)
+[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/qsvaR.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/qsvaR)
 <!-- badges: end -->
 
-The goal of `DeDHeD` is to ...
+The goal of `qsvaR` is to ...
 
 ## Installation instructions
 
-Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `DeDHeD` using from [Bioconductor](http://bioconductor.org/) the following code:
+Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `qsvaR` using from [Bioconductor](http://bioconductor.org/) the following code:
 
 ```{r 'install', eval = FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE)) {
     install.packages("BiocManager")
 }
 
-BiocManager::install("DeDHeD")
+BiocManager::install("qsvaR")
 ```
 
-And the development version from [GitHub](https://github.com/LieberInstitute/DeDHed) with:
+And the development version from [GitHub](https://github.com/LieberInstitute/qsvaR) with:
 
 ```{r 'install_dev', eval = FALSE}
-BiocManager::install("LieberInstitute/DeDHed")
+BiocManager::install("LieberInstitute/qsvaR")
 ```
 ## Example
 
 This is a basic example which shows you how to solve a common problem:
 
-```{r example, eval = requireNamespace('DeDHeD')}
-library("DeDHeD")
+```{r example, eval = requireNamespace('qsvaR')}
+library("qsvaR")
 ## basic example code
 ```
 
@@ -66,24 +66,24 @@ In that case, don't forget to commit and push the resulting figure files, so the
 
 ## Citation
 
-Below is the citation output from using `citation('DeDHeD')` in R. Please
-run this yourself to check for any updates on how to cite __DeDHeD__.
+Below is the citation output from using `citation('qsvaR')` in R. Please
+run this yourself to check for any updates on how to cite __qsvaR__.
 
-```{r 'citation', eval = requireNamespace('DeDHeD')}
-print(citation('DeDHeD'), bibtex = TRUE)
+```{r 'citation', eval = requireNamespace('qsvaR')}
+print(citation('qsvaR'), bibtex = TRUE)
 ```
 
-Please note that the `DeDHeD` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
+Please note that the `qsvaR` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.
 
 ## Code of Conduct
 
-Please note that the `DeDHeD` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
+Please note that the `qsvaR` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.
 
 ## Development tools
 
 * Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
 * Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
-* The [documentation website](http://LieberInstitute.github.io/DeDHeD) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
+* The [documentation website](http://LieberInstitute.github.io/qsvaR) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
 * The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
 * The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
 

diff --git a/README.md b/README.md
@@ -1,45 +1,45 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# DeDHeD
+# qsvaR
 
 <!-- badges: start -->
 
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![BioC
-status](http://www.bioconductor.org/shields/build/release/bioc/DeDHeD.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/DeDHeD)
+status](http://www.bioconductor.org/shields/build/release/bioc/qsvaR.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/qsvaR)
 <!-- badges: end -->
 
-The goal of `DeDHeD` is to …
+The goal of `qsvaR` is to …
 
 ## Installation instructions
 
 Get the latest stable `R` release from
-[CRAN](http://cran.r-project.org/). Then install `DeDHeD` using from
+[CRAN](http://cran.r-project.org/). Then install `qsvaR` using from
 [Bioconductor](http://bioconductor.org/) the following code:
 
 ``` r
 if (!requireNamespace("BiocManager", quietly = TRUE)) {
     install.packages("BiocManager")
 }
 
-BiocManager::install("DeDHeD")
+BiocManager::install("qsvaR")
 ```
 
 And the development version from
-[GitHub](https://github.com/LieberInstitute/DeDHed) with:
+[GitHub](https://github.com/LieberInstitute/qsvaR) with:
 
 ``` r
-BiocManager::install("LieberInstitute/DeDHed")
+BiocManager::install("LieberInstitute/qsvaR")
 ```
 
 ## Example
 
 This is a basic example which shows you how to solve a common problem:
 
 ``` r
-library("DeDHeD")
+library("qsvaR")
 #> Loading required package: SummarizedExperiment
 #> Loading required package: MatrixGenerics
 #> Loading required package: matrixStats
@@ -135,27 +135,27 @@ files, so they display on GitHub!
 
 ## Citation
 
-Below is the citation output from using `citation('DeDHeD')` in R.
+Below is the citation output from using `citation('qsvaR')` in R.
 Please run this yourself to check for any updates on how to cite
-**DeDHeD**.
+**qsvaR**.
 
 ``` r
-print(citation('DeDHeD'), bibtex = TRUE)
+print(citation('qsvaR'), bibtex = TRUE)
 #> 
-#> LieberInstitute (2021). _TODO_. doi: 10.18129/B9.bioc.DeDHeD (URL:
-#> https://doi.org/10.18129/B9.bioc.DeDHeD),
-#> https://github.com/LieberInstitute/DeDHed/DeDHeD - R package version
-#> 0.99.0, <URL: http://www.bioconductor.org/packages/DeDHeD>.
+#> LieberInstitute (2021). _TODO_. doi: 10.18129/B9.bioc.qsvaR (URL:
+#> https://doi.org/10.18129/B9.bioc.qsvaR),
+#> https://github.com/LieberInstitute/qsvaR/qsvaR - R package version
+#> 0.99.0, <URL: http://www.bioconductor.org/packages/qsvaR>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
 #>     title = {TODO},
 #>     author = {{LieberInstitute}},
 #>     year = {2021},
-#>     url = {http://www.bioconductor.org/packages/DeDHeD},
-#>     note = {https://github.com/LieberInstitute/DeDHed/DeDHeD - R package version 0.99.0},
-#>     doi = {10.18129/B9.bioc.DeDHeD},
+#>     url = {http://www.bioconductor.org/packages/qsvaR},
+#>     note = {https://github.com/LieberInstitute/qsvaR/qsvaR - R package version 0.99.0},
+#>     doi = {10.18129/B9.bioc.qsvaR},
 #>   }
 #> 
 #> LieberInstitute (2021). "TODO." _bioRxiv_. doi: 10.1101/TODO (URL:
@@ -174,13 +174,13 @@ print(citation('DeDHeD'), bibtex = TRUE)
 #>   }
 ```
 
-Please note that the `DeDHeD` was only made possible thanks to many
+Please note that the `qsvaR` was only made possible thanks to many
 other R and bioinformatics software authors, which are cited either in
 the vignettes and/or the paper(s) describing this package.
 
 ## Code of Conduct
 
-Please note that the `DeDHeD` project is released with a [Contributor
+Please note that the `qsvaR` project is released with a [Contributor
 Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By
 contributing to this project, you agree to abide by its terms.
 
@@ -197,7 +197,7 @@ contributing to this project, you agree to abide by its terms.
 -   Code coverage assessment is possible thanks to
     [codecov](https://codecov.io/gh) and
     *[covr](https://CRAN.R-project.org/package=covr)*.
--   The [documentation website](http://LieberInstitute.github.io/DeDHeD)
+-   The [documentation website](http://LieberInstitute.github.io/qsvaR)
     is automatically updated thanks to
     *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
 -   The code is styled automatically thanks to

diff --git a/dev/01_create_pkg.R b/dev/01_create_pkg.R
@@ -52,11 +52,11 @@ if (!requireNamespace("BiocStyle", quietly = TRUE)) {
 
 
 ## Package names have some properties. You can also use:
-available::available("DeDHeD")
+available::available("qsvaR")
 ## to check that your package name is not taken and that it doesn't have
 ## a meaning that you might not be aware of.
 
-usethis::create_package("DeDHeD")
+usethis::create_package("qsvaR")
 ## This opens a new window in RStudio
 
 ## Note: If you create packages frequently, check the help file for

diff --git a/inst/CITATION b/inst/CITATION
@@ -1,7 +1,7 @@
 pkgVer <- function(pkg) {
     if (!exists("meta") || is.null(meta)) meta <- packageDescription(pkg)
     ver <- meta$Version
-    paste0('https://github.com/LieberInstitute/DeDHed/', pkg, ' - R package version ', ver)
+    paste0('https://github.com/LieberInstitute/qsvaR/', pkg, ' - R package version ', ver)
 }
 
 c(
@@ -12,9 +12,9 @@ c(
             as.person("LieberInstitute")
         ),
         year = format(Sys.Date(), "%Y"),
-        url = "http://www.bioconductor.org/packages/DeDHeD",
-        note = pkgVer('DeDHeD'),
-        doi = '10.18129/B9.bioc.DeDHeD'
+        url = "http://www.bioconductor.org/packages/qsvaR",
+        note = pkgVer('qsvaR'),
+        doi = '10.18129/B9.bioc.qsvaR'
     ),
     bibentry(bibtype="article",
         title = "TODO",