adjustLogRatio: Adjust tumor vs. normal coverage log ratio for tumor purity...

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

Adjust tumor vs. normal coverage log ratio for tumor purity and ploidy

Description

This function can be used to adjust the log ratio for tumor purity and ploidy for downstream tools that expect a log2 ratio (for example GISTIC).

Usage

adjustLogRatio(ratio, purity, ploidy, is.log2 = TRUE, min.ratio = 2^-8)

Arguments

ratio	Vector of log2 tumor vs normal coverage ratios.
purity	Purity of sample.
ploidy	Ploidy of sample.
is.log2	log.ratio is log2 transformed.
min.ratio	Minimum (non-log2-transformed) ratio. Set to approx -8 log2 adjusted.

Value

numeric(length(log.ratio)), log.ratio adjusted for purity and ploidy

Author(s)

Markus Riester

References

Nature Biotechnology. * Toal (2018), https://github.com/lima1/PureCN/issues/40

Examples

normal.coverage.file <- system.file("extdata", "example_normal.txt.gz", 
    package = "PureCN")
tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz", 
    package = "PureCN")
normal <- readCoverageFile(normal.coverage.file)
tumor <- readCoverageFile(tumor.coverage.file)
log.ratio <- calculateLogRatio(normal, tumor)
log.ratio.adjusted <- adjustLogRatio(log.ratio, 0.65, 1.73)

lima1/PureCN documentation built on April 24, 2024, 8:23 p.m.