NegativeBinomialTestWithReplicate: Negative binomial test of binding using all replicates

In ManchesterBioinference/Motif2Site: Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Description

Adapted exact test function from edgeR to compare IP vs Input with replicates. Input is a DGELIST with common and tag-wise dispression has been already caluclated by edgeR commands.

It calculates abundaces with mglmOneGroup identical to edgeR. logFE was calculated identiacl to edgeR. For the pvalue test negative binomial test is performed on the calculated abundance.

Usage

NegativeBinomialTestWithReplicate(object, prior.count = 0.125)

Arguments

object	Table of counts which contains all IP and Input value counts, TMM normalized and contains dispersion values
prior.count	edgeR prior value

Value

log fold enrichment, pvalue, and normalized count values

ManchesterBioinference/Motif2Site documentation built on Feb. 13, 2022, 2:03 a.m.