matrixShuffleZscorePerSequence {PWMEnrich}R Documentation

Obtain z-score for motif column shuffling

Description

All PWMs are shuffled at the same time. This function would be too slow to produce empirical P-values, thus we return a z-score from a small number of shuffles.

Usage

matrixShuffleZscorePerSequence(scores, sequences, pwms, cutoff = NULL, B = 30)

Arguments

scores

a set of already calculated scores

sequences

either one sequence or a list/set of sequences (objects of type DNAString or DNAStringSet)

pwms

a list of PWMs

cutoff

if NULL, will use affinity, otherwise will use number of hits over this log2 odds cutoff

B

number of replicates, i.e. PWM column shuffles

Details

The z-scores are calculated for each sequence individually.


[Package PWMEnrich version 4.26.0 Index]