empiricalPvalue {PWMEnrich} | R Documentation

## Calculate the empirical P-value by affinity of cutoff.

### Description

This is the new backend function for empirical P-values for either affinity or cutoff. The function only works on single sequences.

### Usage

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

### Arguments

`scores` | the scores obtained for the sequence
`seq.len` | the length of the sequence, if a single value will take a single sequence of given length. If a vector of values, will take sequences of given lengths and joint them together
`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
`exact.length` | if to take into consideration that the actual sequence lengths differ for different PWMs. For very long sequences (i.e. seq.len >> pwm.len) this make very little difference, however the run time with exact.length is much longer.

[Package PWMEnrich version 4.28.1 Index]