Fix fit_elements for new BCalm release

.Rbuildignore

@@ -1,3 +1,8 @@
-^\.travis\.yml$
+.editorconfig
+.gitignore
+.lintr
+.yamllint.yml
+^\.\.Rcheck
+.git
+.github
 README.md
-

.editorconfig

@@ -0,0 +1,48 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+trim_trailing_whitespace = true
+
+# R files
+[*.R]
+indent_style = space
+indent_size = 4
+max_line_length = 127
+
+# Rmd files (R Markdown)
+[*.Rmd]
+indent_style = space
+indent_size = 2
+max_line_length = 127
+
+# YAML files
+[*.{yml,yaml}]
+indent_style = space
+indent_size = 2
+
+# JSON files
+[*.json]
+indent_style = space
+indent_size = 2
+
+# Markdown files
+[*.md]
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = false
+
+# Makefile
+[Makefile]
+indent_style = tab
+
+# Shell scripts
+[*.sh]
+indent_style = space
+indent_size = 2

.github/workflows/labeler.yml

@@ -0,0 +1,13 @@
+---
+name: "Pull Request Labeler"
+on: # yamllint disable-line rule:truthy
+  pull_request_target:
+
+jobs:
+  labeler:
+    permissions:
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/labeler@v6

.github/workflows/main.yml

@@ -0,0 +1,28 @@
+---
+name: Tests
+
+on: # yamllint disable-line rule:truthy
+  push:
+    branches: [master, development]
+  pull_request:
+    branches: [master, development]
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - name: Formatting
+        uses: super-linter/super-linter@v8
+        env:
+          LINTER_RULES_PATH: .
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: master
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SAVE_SUPER_LINTER_SUMMARY: true
+          VALIDATE_JSON: true
+          VALIDATE_YAML: true
+          YAML_CONFIG_FILE: .yamllint.yml
+          VALIDATE_R: true

.github/workflows/pkgdown.yml

@@ -0,0 +1,34 @@
+---
+name: pkgdown
+on: # yamllint disable-line rule:truthy
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  release:
+    types: [published]
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v6
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs

.github/workflows/r-cmd-check.yml

@@ -0,0 +1,28 @@
+---
+name: R-CMD-check
+on: # yamllint disable-line rule:truthy
+  push:
+    branches: [master, development]
+  pull_request:
+    branches: [master, development]
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'devel'}
+          # - {os: macos-latest, r: 'release'}
+          # - {os: windows-latest, r: 'release'}
+    steps:
+      - uses: actions/checkout@v6
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/spellcheck.yml

@@ -0,0 +1,24 @@
+---
+name: Spell Check
+on: # yamllint disable-line rule:truthy
+  push:
+    branches: [master, development]
+  pull_request:
+    branches: [master, development]
+
+jobs:
+  spellcheck:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: r-lib/actions/setup-r@v2
+      - name: Install spelling package
+        run: Rscript -e 'install.packages("spelling")'
+      - name: Check spelling
+        run: Rscript -e 'spelling::spell_check_package()'
+      - name: Check for spelling errors
+        run: |
+          if [ -s spelling.txt ]; then
+            cat spelling.txt
+            exit 1
+          fi

.github/workflows/test-coverage.yml

@@ -0,0 +1,38 @@
+---
+name: test-coverage
+on: # yamllint disable-line rule:truthy
+  push:
+    branches: [master, development]
+  pull_request:
+    branches: [master, development]
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v6
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+      - name: Show testthat output
+        if: always()
+        run: |
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -7,4 +7,5 @@ auto/
 .DS_Store
 inst/doc
 *.pdf
-*.html
+*.html
+..Rcheck

.lintr

@@ -0,0 +1,7 @@
+linters: linters_with_defaults(
+  line_length_linter(127),
+  indentation_linter(indent = 4),
+  commented_code_linter = NULL,
+  object_usage_linter = NULL,
+  object_name_linter = NULL
+  )

.yamllint.yml

@@ -0,0 +1,10 @@
+---
+extends: default
+
+rules:
+  # 80 chars should be enough, but don't fail if a line is longer
+  line-length:
+    max: 127
+    level: warning
+  comments:
+    min-spaces-from-content: 1

DESCRIPTION

@@ -1,17 +1,18 @@
 Package: BCalm
 Version: 0.99.0
-Title: Barcode Analysis using linear models
-Description: Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).
+Title: Barcode Analysis Using Linear Models
+Description: Tools for data management, count preprocessing, and differential analysis in massively parallel reporter assays (MPRA).
 Authors@R: c(
       person("Pia", "Keukeleire", role = c("cre", "aut"), email = "[email protected]"),
       person("Martin", "Kircher", role = "aut"))
+Author: Pia Keukeleire [cre, aut], Martin Kircher [aut]
+Maintainer: Pia Keukeleire <[email protected]>
 Depends:
       R (>= 3.5),
       methods,
       BiocGenerics,
       SummarizedExperiment,
-      limma,
-      curl
+      limma
 Suggests:
       BiocStyle,
       knitr,
@@ -28,19 +29,16 @@ Imports:
       graphics,
       statmod,
       tidyr,
-      GenomeInfoDb,
-      IRanges,
-      GenomicRanges,
-      Biobase,
-      DelayedArray
+      dplyr,
+      rlang
 Collate:
       mpra_set.R
       utils.R
       fit.R
       preprocess.R
       analyze.R
 VignetteBuilder: knitr
-License: MIT
+License: MIT + file LICENSE
 URL: https://github.com/kircherlab/BCalm
 BugReports: https://github.com/kircherlab/BCalm/issues
 biocViews: Software, GeneRegulation, Sequencing, FunctionalGenomics

LICENSE

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

NAMESPACE

@@ -5,15 +5,15 @@ import(limma, except = "plotMA")
 import(S4Vectors)
 importFrom("scales", "alpha")
 importFrom("graphics", "lines")
-importFrom("stats", "approxfun", "lowess")
+importFrom("stats", "approxfun", "lowess", "pt", "quantile", "setNames")
 importFrom("statmod", "mixedModel2Fit")
 importFrom("tidyr", "pivot_wider")
 importFrom("tidyr", "unite")
+importFrom("dplyr", "%>%", "group_by", "summarise", "mutate", "filter", "ungroup", "pull", "select", "n", "row_number", "arrange", "matches", "rename_with")
+importFrom("rlang", "sym")
 importFrom("mpra", MPRASet, getRNA, getDNA, getBarcode, getEid, getEseq, normalize_counts, mpralm, get_precision_weights)
 
-exportClasses("MPRASet")
-exportMethods("show")
 export(MPRASet, getRNA, getDNA, getBarcode, getEid, getEseq, getLabel)
 export(mpralm, get_precision_weights, compute_logratio, normalize_counts, fit_elements)
 export(downsample_barcodes, create_dna_df, create_rna_df, create_var_df)
-export(plot_groups, mpra_treat)
+export(plot_groups, mpra_treat)