cn2lr-methods: Take vector or matrix of copynumber values, convert to...

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

Utility function for converting copynumber units (2 is normal) to log2ratio units (two is normal). If ploidy is provided lr is log2(cn/ploidy), otherwise log2(cn/2).

Usage

cn2lr(x, ploidy)

## S4 method for signature 'numeric'
cn2lr(x, ploidy)

## S4 method for signature 'matrix'
cn2lr(x, ploidy)

## S4 method for signature 'DataFrame'
cn2lr(x, ploidy)

Arguments

x	numeric vector or matrix, or DataFrame with numeric-like columns (Rle typicaly). Assumed to be in copynumber units.
ploidy	numeric, of length ncol(x). Ploidy of each sample.

Value

data of same type as 'x' transformed into log2ratio units

See Also

lr2cn

genoset documentation built on Nov. 8, 2020, 6:07 p.m.