genoset (version 1.28.2)

gcCorrect: Correct copy number for GC content

Description

Copy number estimates from various platforms show "Genomic Waves" (Diskin et al., Nucleic Acids Research, 2008, PMID: 18784189) where copy number trends with local GC content. This function regresses copy number on GC percentage and removes the effect (returns residuals). GC content should be smoothed along the genome in wide windows >= 100kb.

Usage

gcCorrect(ds, gc, retain.mean = TRUE)

Arguments

ds

numeric matrix of copynumber or log2ratio values, samples in columns

gc

numeric vector, GC percentage for each row of ds, must not have NAs

retain.mean

logical, center on zero or keep same mean?

Value

• numeric matrix, residuals of ds regressed on gc

Examples

gc = runif(n=100, min=1, max=100)
  ds = rnorm(100) + (0.1 * gc)
  gcCorrect(ds, gc)