getLibsize: Get read counts for each sample from the bam files.

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

Get read counts for each sample from the bam files.

Description

Get read counts for each sample from the bam files.

Usage

getLibsize(SampleID, bamFils, nCore = 1)

Arguments

SampleID	Matrix representing the raw read counts for samples. Row are the peaks, column are the samples
lib.size	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.
group	vector or factor giving the experimental group/condition for each sample/library. If it is null,no control/condition are used.

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.