tmm_matrix: Use edgeR to do TMM normalization with or without full...

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

Use edgeR to do TMM normalization with or without full library size

Description

Use edgeR to do TMM normalization with or without full library size

Usage

tmm_matrix(counts, lib.size = NULL, group = c(rep(1, 3), rep(2, 3)))

Arguments

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.
rawcount	Matrix representing the raw read counts for samples. Row are the peaks, column are the samples

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.