get_pLOH_score: Get proportions of pLOH score from Allele Specific Copy...

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Get proportions of pLOH score from Allele Specific Copy Number Profile

Description

pLOH score represents the genome that displayed LOH.

Usage

get_pLOH_score(data, rm_chrs = c("chrX", "chrY"), genome_build = "hg19")

Arguments

data	a CopyNumber object or a data.frame containing at least 'chromosome', 'start', 'end', 'segVal', "minor_cn", 'sample' these columns.
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'.

Value

A data.frame

References

Steele, Christopher D., et al. "Signatures of copy number alterations in human cancer." bioRxiv (2021).

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

sigminer documentation built on May 29, 2024, 3:11 a.m.