consDESeq2_DM {exomePeak2} | R Documentation

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

### 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.

[Package exomePeak2 version 1.2.0 Index]