cpmNorm: Do log2CPM normalization with or without full library size

In yancychy/DiffChIPL: ChIP-seq differential analysis (DiffChIPL)

Do log2CPM normalization with or without full library size

Description

Do log2CPM normalization with or without full library size

Usage

cpmNorm(rawcount, libsize = NULL)

Arguments

rawcount	Matrix representing the raw read counts for samples. Row are the peaks, column are the samples
libsize	Numeric vector representing the full library size for all samples. If it is null, use the sum of read count in each sample as the library size. By default, user should use full library size to scale the read counts

Value

normalized read counts (log2(read counts / sum of read counts + 1)) .

Examples

cpmD = cpmNorm(countAll)

# The robustness.
cpmD = cpmNorm(countAll, libsize=fd$lsIP)
cpmD = cpmNorm(countAll)

yancychy/DiffChIPL documentation built on Dec. 24, 2024, 11:26 p.m.