consDESeq2_M {exomePeak2} | R Documentation |
Calculate the index for across sample modification consistency in a DESeqDataSet object
consDESeq2_M( dds, consistent_log2FC_cutoff = 1, consistent_fdr_cutoff = 0.05, p0 = 0.8, alpha = 0.05 )
dds |
a DESeqDataSet object. |
consistent_log2FC_cutoff |
a |
consistent_fdr_cutoff |
a |
p0 |
a For a peak to be consistently methylated, the minimum number of significant enriched replicate pairs is defined as the 1 - alpha quantile of a binomial distribution with p = p0 and N = number of possible pairs between replicates. The consistency defined in this way is equivalent to the rejection of an exact binomial test with null hypothesis of p < p0 and N = replicates number of IP * replicates number of input. |
alpha |
a |
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.