consDESeq2_DM: Calculate the index for across sample differential...

In exomePeak2: Bias Awared Peak Calling and Quantification for MeRIP-Seq

Description

Calculate the index for across sample differential modification consistency in a DESeqDataSet object

Usage

consDESeq2_DM(dds, consistent_log2FC_cutoff = 1, p = 0.7, alpha = 0.05)

Arguments

dds	a DESeqDataSet object.
consistent_log2FC_cutoff	a numeric for the cutoff of differential modification log2 fold changes; default = 1.
p	the binomial parameter p used by the binomial test; default = 0.7.
alpha	the significant level of the binomial test; default = 0.05.

Details

The minimum consistent number cutcoff is defined by 1-alpha quantile of a binomial distribution with probability of success = p, and number of trials = number of possible pairs between replicates. This is equivalent to the rejection of an exact binomial test with null hypothesis of p < 0.8 and N = number of possible pairs.

Value

a logical index for the consistently modified rows in the DESeqDataSet.

exomePeak2 documentation built on Nov. 8, 2020, 5:27 p.m.