consDESeq2_DM {exomePeak2} | R Documentation |
Calculate the index for across sample differential modification consistency in a DESeqDataSet object
consDESeq2_DM(dds, consistent_log2FC_cutoff = 1, p = 0.7, alpha = 0.05)
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. |
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.
a logical index for the consistently modified rows in the DESeqDataSet.