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montilab · Mar 14, 2024 · 134a61e · 134a61e
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diff --git a/.Rbuildignore b/.Rbuildignore
diff --git a/.dockerignore b/.dockerignore
diff --git a/.github/workflows/R-CMD-CHECK.yaml b/.github/workflows/R-CMD-CHECK.yaml
diff --git a/.github/workflows/document.yaml b/.github/workflows/document.yaml
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
diff --git a/.github/workflows/render-news-rmd.yml b/.github/workflows/render-news-rmd.yml
diff --git a/.github/workflows/render-readme-rmd.yml b/.github/workflows/render-readme-rmd.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -20,38 +20,36 @@ Description: Performs both stepwise and backward heuristic search for
     continuous scores (e.g. sample-specific scores representing a phenotypic 
     readout of interest, such as protein expression, pathway activity, etc.), 
     based on the union occurence (i.e. logical OR) of the events.
-Depends: R (>= 4.1.0)
+Depends: R (>= 4.3.0)
 LazyData: false
 License: GPL-3 + file LICENSE
 URL: https://github.com/montilab/CaDrA/
 Packaged: 2022-11-20 18:35:45 UTC; 
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports: 
-    doParallel, 
-    ggplot2,
-    gplots,
-    graphics, 
-    grid, 
-    gtable,
-    MASS, 
-    methods,
-    misc3d,
-    plyr,
-    ppcor, 
-    R.cache,
-    reshape2,
-    stats, 
-    SummarizedExperiment 
+  doParallel, 
+  ggplot2,
+  gplots,
+  graphics, 
+  grid, 
+  gtable,
+  MASS, 
+  methods,
+  misc3d,
+  plyr,
+  ppcor, 
+  R.cache,
+  reshape2,
+  stats, 
+  SummarizedExperiment 
 Suggests: 
-    BiocManager,
-    BiocStyle,
-    devtools,
-    knitr,
-    magick,
-    pheatmap,
-    rmarkdown,
-    testthat (>= 3.1.6)
+  BiocManager,
+  devtools,
+  knitr,
+  pheatmap,
+  rmarkdown,
+  testthat (>= 3.1.6)
 Config/testthat/edition: 3
 biocViews: Microarray, RNASeq, GeneExpression, Software, FeatureExtraction
 VignetteBuilder: knitr

diff --git a/Dockerfile b/Dockerfile
diff --git a/NEWS.md b/NEWS.md
diff --git a/R/BRCA_GISTIC_MUT_SIG.R b/R/BRCA_GISTIC_MUT_SIG.R
diff --git a/R/CCLE_MUT_SCNA.R b/R/CCLE_MUT_SCNA.R
diff --git a/R/CTNBB1_reporter.R b/R/CTNBB1_reporter.R
diff --git a/R/TAZYAP_BRCA_ACTIVITY.R b/R/TAZYAP_BRCA_ACTIVITY.R
diff --git a/R/cadra.R b/R/cadra.R
diff --git a/R/cadra_functions.R b/R/cadra_functions.R
diff --git a/R/calc_rowscore.R b/R/calc_rowscore.R
diff --git a/R/candidate_search.R b/R/candidate_search.R
diff --git a/R/custom_rowscore.R b/R/custom_rowscore.R
diff --git a/R/ks_rowscore.R b/R/ks_rowscore.R
diff --git a/R/meta_plot.R b/R/meta_plot.R
diff --git a/R/perm_res.R b/R/perm_res.R
diff --git a/R/permutation_plot.R b/R/permutation_plot.R
diff --git a/R/revealer_rowscore.R b/R/revealer_rowscore.R
diff --git a/R/sim_FS.R b/R/sim_FS.R
diff --git a/R/sim_scores.R b/R/sim_scores.R
diff --git a/R/topn_best.R b/R/topn_best.R
diff --git a/R/topn_list.R b/R/topn_list.R
diff --git a/R/topn_plot.R b/R/topn_plot.R
diff --git a/R/wilcox_rowscore.R b/R/wilcox_rowscore.R
diff --git a/README.Rmd b/README.Rmd
diff --git a/_pkgdown.yml b/_pkgdown.yml
diff --git a/data/BRCA_GISTIC_MUT_SIG.rda b/data/BRCA_GISTIC_MUT_SIG.rda
diff --git a/data/TAZYAP_BRCA_ACTIVITY.rda b/data/TAZYAP_BRCA_ACTIVITY.rda
diff --git a/data/perm_res.rda b/data/perm_res.rda
diff --git a/data/sim_FS.rda b/data/sim_FS.rda
diff --git a/data/sim_Scores.rda b/data/sim_Scores.rda
diff --git a/data/topn_list.rda b/data/topn_list.rda
diff --git a/docker-compose.yml b/docker-compose.yml
diff --git a/install_r_packages.R b/install_r_packages.R
diff --git a/man/BRCA_GISTIC_MUT_SIG.Rd b/man/BRCA_GISTIC_MUT_SIG.Rd
diff --git a/man/CaDrA.Rd b/man/CaDrA.Rd
diff --git a/man/TAZYAP_BRCA_ACTIVITY.Rd b/man/TAZYAP_BRCA_ACTIVITY.Rd
diff --git a/man/calc_rowscore.Rd b/man/calc_rowscore.Rd
diff --git a/man/figures/summarize-1.png b/man/figures/summarize-1.png
diff --git a/man/figures/visualize.best-1.png b/man/figures/visualize.best-1.png
diff --git a/man/perm_res.Rd b/man/perm_res.Rd
diff --git a/man/sim_FS.Rd b/man/sim_FS.Rd
diff --git a/man/sim_Scores.Rd b/man/sim_Scores.Rd
diff --git a/man/topn_list.Rd b/man/topn_list.Rd
diff --git a/tests/data/create_toy.R b/tests/data/create_toy.R
diff --git a/tests/data/create_toy.old.R b/tests/data/create_toy.old.R
diff --git a/tests/data/create_toy2.R b/tests/data/create_toy2.R
diff --git a/tests/data/toy_dataset.csv b/tests/data/toy_dataset.csv
diff --git a/tests/data/toy_dataset.rds b/tests/data/toy_dataset.rds
diff --git a/tests/data/toy_dataset2.csv b/tests/data/toy_dataset2.csv
diff --git a/tests/data/toy_dataset2.rds b/tests/data/toy_dataset2.rds
diff --git a/tests/testthat/test-cadra.R b/tests/testthat/test-cadra.R
diff --git a/tests/testthat/test-candidate_search.R b/tests/testthat/test-candidate_search.R
diff --git a/tests/testthat/test-check_top_N.R b/tests/testthat/test-check_top_N.R
diff --git a/tests/testthat/test-custom_rowscore.R b/tests/testthat/test-custom_rowscore.R
diff --git a/tests/testthat/test-generate_permutations.R b/tests/testthat/test-generate_permutations.R
diff --git a/tests/testthat/test-ks_plot.R b/tests/testthat/test-ks_plot.R
@@ -16,7 +16,6 @@ test_that("ks_plot works", {
   # Plot the enrichment scores
   g <- ks_plot(df = ks_enrichment_coordinates)
   expect_type(g, "list")
-  expect_length(g, 9L)
   expect_s3_class(g$layers[[1]], "LayerInstance")
   expect_s3_class(g$layers[[1]]$geom, "GeomLine")
   expect_s3_class(g$layers[[2]], "LayerInstance")

diff --git a/tests/testthat/test-ks_rowscore.R b/tests/testthat/test-ks_rowscore.R
diff --git a/tests/testthat/test-meta_plot.R b/tests/testthat/test-meta_plot.R
diff --git a/tests/testthat/test-permutation_plot.R b/tests/testthat/test-permutation_plot.R
@@ -6,7 +6,6 @@ test_that("permutation_plot works", {
   g <- permutation_plot(perm_res)
 
   expect_type(g, "list")
-  expect_length(g, 9L)
   expect_s3_class(g$layers[[1]], "LayerInstance")
   expect_s3_class(g$layers[[1]]$geom, "GeomBar")
   expect_s3_class(g$layers[[2]], "LayerInstance")

diff --git a/tests/testthat/test-prefilter_data.R b/tests/testthat/test-prefilter_data.R
diff --git a/tests/testthat/test-revealer_rowscore.R b/tests/testthat/test-revealer_rowscore.R
diff --git a/tests/testthat/test-topn_best.R b/tests/testthat/test-topn_best.R
diff --git a/tests/testthat/test-topn_plot.R b/tests/testthat/test-topn_plot.R
diff --git a/tests/testthat/test-wilcox_rowscore.R b/tests/testthat/test-wilcox_rowscore.R
diff --git a/vignettes/docker.Rmd b/vignettes/docker.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "How to run CaDrA within a Docker Environment"
-output: BiocStyle::html_document
+output: rmarkdown::html_document
 vignette: >
   %\VignetteIndexEntry{How to run CaDrA within a Docker Environment}
   %\VignetteEngine{knitr::rmarkdown}

diff --git a/vignettes/permutation_based_testing.Rmd b/vignettes/permutation_based_testing.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "Permutation-Based Testing"
-output: BiocStyle::html_document
+output: rmarkdown::html_document
 vignette: >
   %\VignetteIndexEntry{Permutation-Based Testing}
   %\VignetteEngine{knitr::rmarkdown}

diff --git a/vignettes/scoring_functions.Rmd b/vignettes/scoring_functions.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "Scoring Functions"
-output: BiocStyle::html_document
+output: rmarkdown::html_document
 vignette: >
   %\VignetteIndexEntry{Scoring Functions}
   %\VignetteEngine{knitr::rmarkdown}