Merge pull request #144 from umccr/add_ppl

Copy gpgr ppl_cnv_som_gene_read over

DESCRIPTION

@@ -20,7 +20,6 @@ License: MIT + file LICENSE
 Depends: 
     R (>= 4.1.0)
 Remotes:
-    umccr/gpgr,
     umccr/RNAsum.data
 Imports:
     AnnotationDbi,
@@ -31,12 +30,11 @@ Imports:
     DT,
     EDASeq,
     edgeR,
-    EnsDb.Hsapiens.v86,
     ensembldb,
     fs,
+    ggforce,
     ggplot2,
     glue,
-    gpgr,
     htmltools,
     htmlwidgets,
     knitr,
@@ -68,5 +66,5 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE,
               roclets = c("namespace", "rd", "roxytest::testthat_roclet"))
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 LazyData: true

NAMESPACE

@@ -38,6 +38,7 @@ export(pca)
 export(pcgr_expr)
 export(pcgr_tiers_tsv_read)
 export(perc_rank)
+export(ppl_cnv_som_gene_read)
 export(prepare2write)
 export(purple_cnv_summary)
 export(rcircos_cyto_info38)

R/sample_data.R

@@ -140,7 +140,7 @@ read_wgs_data <- function(p) {
   purple_gene_tsv <- .read(
     p = p,
     subdir = "purple", pat = "purple\\.cnv\\.gene\\.tsv$",
-    nm = "purple_gene_tsv", func = gpgr::purple_cnv_som_gene_read
+    nm = "purple_gene_tsv", func = ppl_cnv_som_gene_read
   )
 
   manta_tsv <- .read(
@@ -324,3 +324,33 @@ immune_summary <- function(tbl_imarkers, tbl_igram = NULL, igram_param = TRUE) {
   res <- unique(c(res1, res2)) |> stats::na.omit()
   res
 }
+
+#' Read PURPLE CNV Gene File
+#'
+#' Reads the `purple.cnv.gene.tsv` file, which summarises copy number
+#' alterations of each gene in the HMF panel
+#' (see https://github.com/hartwigmedical/hmftools/tree/master/purple#gene-copy-number-file).
+#'
+#' @param x Path to `purple.cnv.gene.tsv` file.
+#'
+#' @return The input file as a tibble.
+#'
+#' @export
+ppl_cnv_som_gene_read <- function(x) {
+  nm <- c(
+    "chromosome" = "c", "start" = "i", "end" = "i", "gene" = "c",
+    "minCopyNumber" = "d", "maxCopyNumber" = "d",
+    "unused" = "c", "somaticRegions" = "d", "germlineHomDeletionRegions" = "d",
+    "germlineHetToHomDeletionRegions" = "d",
+    "transcriptId" = "c", "transcriptVersion" = "c", "chromosomeBand" = "c",
+    "minRegions" = "d", "minRegionStart" = "i", "minRegionEnd" = "i",
+    "minRegionStartSupport" = "c", "minRegionEndSupport" = "c",
+    "minRegionMethod" = "c", "minMinorAlleleCopyNumber" = "d"
+  )
+
+  ctypes <- paste(nm, collapse = "")
+  purple_cnv_gene <- readr::read_tsv(x, col_types = ctypes)
+  assertthat::assert_that(ncol(purple_cnv_gene) == length(nm))
+  assertthat::assert_that(all(colnames(purple_cnv_gene) == names(nm)))
+  purple_cnv_gene
+}

deploy/conda/recipe/meta.yaml

@@ -21,17 +21,16 @@ requirements:
     - bioconductor-annotationfilter
     - r-assertthat
     - r-conflicted
-    - r-dt
     - r-dplyr
+    - r-dt
     - bioconductor-edaseq ==2.28.0
-    - bioconductor-ensdb.hsapiens.v86
     - bioconductor-edger ==3.36.0
     - bioconductor-ensembldb
     - r-fs
     - r-ggforce
     - r-ggplot2
     - r-glue
-    - umccr::r-gpgr
+    - r-here
     - r-htmltools
     - r-htmlwidgets
     - r-knitr
@@ -61,17 +60,16 @@ requirements:
     - bioconductor-annotationfilter
     - r-assertthat
     - r-conflicted
-    - r-dt
     - r-dplyr
+    - r-dt
     - bioconductor-edaseq ==2.28.0
-    - bioconductor-ensdb.hsapiens.v86
     - bioconductor-edger ==3.36.0
     - bioconductor-ensembldb
     - r-fs
     - r-ggforce
     - r-ggplot2
     - r-glue
-    - umccr::r-gpgr
+    - r-here
     - r-htmltools
     - r-htmlwidgets
     - r-knitr

inst/rmd/.gitignore

@@ -1,3 +1,3 @@
-rnasum.html
 rnasum_files/
 rnasum.md
+/html/

tests/testthat/test-roxytest-testexamples-sample_data.R

@@ -18,7 +18,7 @@ test_that("Function read_sample_data() @ L27", {
 })
 
 
-test_that("Function read_wgs_data() @ L103", {
+test_that("Function read_wgs_data() @ L107", {
 
   p <- list(
     umccrise = system.file("rawdata/test_data/umccrised/test_sample_WGS", package = "RNAsum"),