gcCorrect: Correct copy number for GC content
In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description Usage Arguments Value Examples

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.

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

`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?

numeric matrix, residuals of ds regressed on gc

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

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