empiricalPvalueSequenceSet {PWMEnrich} | R Documentation

## Empirical P-value for a set of sequences

### Description

Calculate empirical P-value for a set of sequences, using either affinity or cutoff. When cutoff is used, the score is a number of motif hits above a certain log-odds cutoff.

### Usage

    empiricalPvalueSequenceSet(
      scores,
      seq.len,
      pwm.len,
      bg.fwd,
      bg.rev,
      cutoff = NULL,
      B = 10000,
      verbose = FALSE
    )

### Arguments

`scores` | a matrix of scores, rows for sequences, columns for PWMs
`seq.len` | the lengths of sequences
`pwm.len` | the lengths of PWMs
`bg.fwd` | raw odds scores for the forward strand of background
`bg.rev` | raw odds scores for the reverse strand of background
`cutoff` | if not NULL, will use hit count above this cutoff. The cutoff should be specified in log2.
`B` | the number of random replicates
`verbose` | if to give verbose progress reports

[Package PWMEnrich version 4.28.1 Index]