Add get_pLOH_score

NAMESPACE

@@ -38,6 +38,7 @@ export(get_genome_annotation)
 export(get_group_comparison)
 export(get_groups)
 export(get_intersect_size)
+export(get_pLOH_score)
 export(get_shannon_diversity_index)
 export(get_sig_cancer_type_index)
 export(get_sig_db)

NEWS.md

@@ -1,5 +1,6 @@
 # sigminer 2.0.5
 
+- Added function `get_pLOH_score()` for representing the genome that displayed LOH.
 - Added function `read_copynumber_ascat()` for reading ASCAT result ASCAT object in `.rds` format.
 - Added function `get_intersect_size()` for getting overlap size between intervals.
 - Added option to `get_Aneuploidy_score()` to remove short arms of chr13/14/15/21/22 from calculation.

R/get_pLOH_score.R

@@ -0,0 +1,61 @@
+#' Get proportions of pLOH score from Allele Specific Copy Number Profile
+#'
+#' pLOH score represents the genome that displayed LOH.
+#'
+#' @inheritParams read_copynumber
+#' @param data a CopyNumber object or a `data.frame` containing at least
+#' 'chromosome', 'start', 'end', 'segVal', 'sample' these columns.
+#' @param rm_chrs chromosomes to be removed in calculation. Default is sex
+#' chromosomes (recommended).
+#' @references
+#' Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." bioRxiv (2021).
+#'
+#' @return A `data.frame`
+#' @export
+#'
+#' @examples
+#' # Load toy dataset of absolute copynumber profile
+#' load(system.file("extdata", "toy_segTab.RData",
+#'   package = "sigminer", mustWork = TRUE
+#' ))
+#'
+#' set.seed(1234)
+#' segTabs$minor_cn <- sample(c(0, 1), size = nrow(segTabs), replace = TRUE)
+#' cn <- read_copynumber(segTabs,
+#'   seg_cols = c("chromosome", "start", "end", "segVal"),
+#'   genome_measure = "wg", complement = TRUE, add_loh = TRUE
+#' )
+#'
+#' df <- get_pLOH_score(cn)
+#' df
+#'
+#' df2 <- get_pLOH_score(cn@data)
+#' df2
+#'
+#' @testexamples
+#' expect_equal(nrow(df), 10L)
+#' expect_equal(nrow(df2), 10L)
+get_pLOH_score <- function(data, rm_chrs = c("chrX", "chrY"), genome_build = "hg19") {
+  stopifnot(is.data.frame(data) | inherits(data, "CopyNumber") | "chrY" %in% rm_chrs)
+  if (!is.data.frame(data)) {
+    data <- data@data
+  }
+
+  nc_cols <- c("chromosome", "start", "end", "segVal", "minor_cn", "sample")
+  if (!all(nc_cols %in% colnames(data))) {
+    stop("Invalid input, it must contain columns: ", paste(nc_cols, collapse = " "))
+  }
+
+  data <- data.table::as.data.table(data)[!chromosome %in% rm_chrs, nc_cols, with = FALSE]
+
+  # Make sure the minor_cn is really minor copy
+  data$minor_cn <- pmin(data$segVal - data$minor_cn, data$minor_cn)
+
+  chr_size <- get_genome_annotation(genome_build = genome_build)
+  chr_size <- chr_size[!chr_size$chrom %in% rm_chrs, ]
+  chr_size <- sum(chr_size$size)
+
+  data[segVal >= 1 & minor_cn == 0, list(pLOH = sum(end - start + 1L) / chr_size), by = "sample"]
+}
+
+

_pkgdown.yml

@@ -149,6 +149,7 @@ reference:
     - transform_seg_table
     - get_cn_ploidy
     - get_Aneuploidy_score
+    - get_pLOH_score
     - scoring
     - show_cn_profile
     - show_cn_circos

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

@@ -0,0 +1,28 @@
+# Generated by roxytest: Do not edit by hand!
+
+# File R/get_pLOH_score.R: @testexamples
+
+test_that("Function get_pLOH_score() @ L38", {
+
+  # Load toy dataset of absolute copynumber profile
+  load(system.file("extdata", "toy_segTab.RData",
+    package = "sigminer", mustWork = TRUE
+  ))
+
+  set.seed(1234)
+  segTabs$minor_cn <- sample(c(0, 1), size = nrow(segTabs), replace = TRUE)
+  cn <- read_copynumber(segTabs,
+    seg_cols = c("chromosome", "start", "end", "segVal"),
+    genome_measure = "wg", complement = TRUE, add_loh = TRUE
+  )
+
+  df <- get_pLOH_score(cn)
+  df
+
+  df2 <- get_pLOH_score(cn@data)
+  df2
+
+  expect_equal(nrow(df), 10L)
+  expect_equal(nrow(df2), 10L)
+})
+