mrnFactors: Use MRN with or without full library size

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

Use MRN with or without full library size

Description

Use MRN with or without full library size

Usage

mrnFactors(rawCounts, conditions, libsize = NULL)

Arguments

conditions	vector or factor giving the experimental group/condition for each sample/library. If it is null,no control/condition are used.
rawcount	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.

Value

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

Examples

cpmD = mrnFactors(countAll,conditions=c(rep(1,2), rep(2,2)), libsize=fd$lsIP)

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