feat: add clean raw counts template (#79)

this is a merge commit

.github/workflows/R-CMD-check.yaml

@@ -28,7 +28,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/auto-format.yml

@@ -0,0 +1,57 @@
+name: auto-format
+
+on:
+  workflow_dispatch:
+  pull_request:
+
+env:
+  GH_TOKEN: ${{ github.token }}
+
+jobs:
+  auto-format:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        if: github.event_name == 'pull_request'
+        with:
+          fetch-depth: 0
+          ref: ${{ github.head_ref }}
+      - uses: actions/checkout@v4
+        if: github.event_name == 'push'
+        with:
+          fetch-depth: 0
+          ref: ${{ github.ref_name }}
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: local::.
+          needs: Suggests
+
+      - name: render README.Rmd
+        shell: Rscript {0}
+        run: |
+          rmarkdown::render("README.Rmd")
+          if (file.exists("README.html")) file.remove("README.html")
+
+      - name: update CITATION.cff
+        shell: Rscript {0}
+        run: |
+          # Customize with your own code
+          # See https://docs.ropensci.org/cffr/articles/cffr.html
+          # Write your own keys
+          mykeys <- list()
+          # Create your CITATION.cff file
+          cffr::cff_write(keys = mykeys)
+
+      - name: format
+        uses: pre-commit/[email protected]
+        continue-on-error: true
+
+      - name: commit & push
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add .
+          git commit -m "ci: 🤖 auto-format" && git push || echo "nothing to commit"

CITATION.cff

@@ -358,6 +358,18 @@ references:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
   year: '2024'
+- type: software
+  title: stringr
+  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
+  notes: Imports
+  url: https://stringr.tidyverse.org
+  repository: https://CRAN.R-project.org/package=stringr
+  authors:
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  year: '2024'
+  doi: 10.32614/CRAN.package.stringr
 - type: software
   title: tibble
   abstract: 'tibble: Simple Data Frames'
@@ -406,6 +418,31 @@ references:
     email: [email protected]
   year: '2024'
   doi: 10.32614/CRAN.package.tidyselect
+- type: software
+  title: cffr
+  abstract: 'cffr: Generate Citation File Format (''cff'') Metadata for R Packages'
+  notes: Suggests
+  url: https://docs.ropensci.org/cffr/
+  repository: https://CRAN.R-project.org/package=cffr
+  authors:
+  - family-names: Hernangómez
+    given-names: Diego
+    email: [email protected]
+    orcid: https://orcid.org/0000-0001-8457-4658
+  year: '2024'
+  doi: 10.32614/CRAN.package.cffr
+- type: software
+  title: docopt
+  abstract: 'docopt: Command-Line Interface Specification Language'
+  notes: Suggests
+  url: https://github.com/docopt/docopt.R
+  repository: https://CRAN.R-project.org/package=docopt
+  authors:
+  - family-names: Jonge
+    given-names: Edwin
+    name-particle: de
+  year: '2024'
+  doi: 10.32614/CRAN.package.docopt
 - type: software
   title: glue
   abstract: 'glue: Interpreted String Literals'
@@ -592,3 +629,16 @@ references:
     orcid: https://orcid.org/0000-0002-7840-692X
   year: '2024'
   doi: 10.32614/CRAN.package.usethis
+- type: software
+  title: V8
+  abstract: 'V8: Embedded JavaScript and WebAssembly Engine for R'
+  notes: Suggests
+  url: https://jeroen.r-universe.dev/V8
+  repository: https://CRAN.R-project.org/package=V8
+  authors:
+  - family-names: Ooms
+    given-names: Jeroen
+    email: [email protected]
+    orcid: https://orcid.org/0000-0002-4035-0289
+  year: '2024'
+  doi: 10.32614/CRAN.package.V8

DESCRIPTION

@@ -33,10 +33,13 @@ Imports:
     rlang,
     S7,
     stats,
+    stringr,
     tibble,
     tidyr,
     tidyselect
 Suggests:
+    cffr,
+    docopt,
     glue,
     knitr,
     lobstr,
@@ -46,7 +49,8 @@ Suggests:
     scales,
     styler,
     testthat (>= 3.0.0),
-    usethis
+    usethis,
+    V8
 VignetteBuilder:
     knitr
 biocViews:

MOSuite.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 8ebbd9db-482e-4f6c-a523-b56383cc5b59
 
 RestoreWorkspace: No
 SaveWorkspace: No

NAMESPACE

@@ -2,11 +2,14 @@
 
 export("%>%")
 export(calc_cpm)
+export(clean_raw_counts)
 export(create_multiOmicDataSet_from_dataframes)
 export(create_multiOmicDataSet_from_files)
 export(filter_counts)
 export(meta_tbl_to_dat)
+export(plot_read_depth)
 export(run_deseq2)
+export(strip_ensembl_version)
 if (getRversion() < "4.3.0") importFrom("S7", "@")
 importFrom(DESeq2,DESeq)
 importFrom(dplyr,"%>%")

NEWS.md

@@ -13,3 +13,4 @@ This is the first release of MOSuite 🎉
 - `run_deseq2()`
 - `calc_cpm()` (#38, @kelly-sovacool)
 - `filter_counts()` (#38, @kelly-sovacool)
+- `clean_raw_counts()` (#79, @kelly-sovacool)

R/0_mo-class.R

@@ -20,7 +20,7 @@ multiOmicDataSet <- S7::new_class("multiOmicDataSet",
   },
   validator = function(self) {
     # counts must only contain approved names
-    approved_counts <- c("raw", "cpm", "filt")
+    approved_counts <- c("raw", "clean", "cpm", "filt")
     if (!all(names(self@counts) %in% approved_counts)) {
       stop(glue::glue("counts can only contain data frames with these names:\n\t{paste(approved_counts, collapse = ', ')}"))
     }