normalizeConsensus {cinaR}

normalizeConsensus

Description

Normalizes consensus peak using different methods

Usage

normalizeConsensus(cp, norm.method = "cpm", log.option = FALSE)

Arguments

cp

bed formatted consensus peak matrix: CHR, START, STOP and raw peak counts (peaks by 3+samples)

norm.method

normalization method for consensus peaks

log.option

logical, log option for cpm function in edgeR

Value

Normalized consensus peaks

Examples

set.seed(123)
cp <- matrix(rexp(200, rate=.1), ncol=20)

## using cpm function from `edgeR` package
cp.normalized <- normalizeConsensus(cp)

## quantile normalization option
cp.normalized <- normalizeConsensus(cp, norm.method = "quantile")