R/get_pLOH_score.R
get_pLOH_score.Rd
pLOH score represents the genome that displayed LOH.
get_pLOH_score(data, rm_chrs = c("chrX", "chrY"), genome_build = "hg19")
data | a CopyNumber object or a |
---|---|
rm_chrs | chromosomes to be removed in calculation. Default is sex chromosomes (recommended). |
genome_build | genome build version, should be 'hg19', 'hg38', 'mm9' or 'mm10'. |
A data.frame
Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." bioRxiv (2021).
# 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