scanWithPWM {PWMEnrich} | R Documentation

## Scan the whole sequence on both strands

### Description

The whole sequence is scanned with a PWM and scores returned beginning at each position. Partial motif matches are not done, thus the last #[length of motif]-1 scores are NA.

### Usage

      scanWithPWM(pwm, dna, pwm.rev = NULL, odds.score = FALSE,
        both.strands = FALSE, strand.fun = "mean")

### Arguments

`pwm` | PWM object
`dna` | a DNAString or other sequence from Biostrings
`pwm.rev` | the reverse complement for a pwm (if it is already pre-computed)
`odds.score` | if to return raw scores in odds (not logodds) space
`both.strands` | if to return results on both strands
`strand.fun` | which function to use to summarise values over two strands (default is "mean")

### Details

The function returns either an odds average (*not* log-odds average), maximal score on each strand, or scores on both strands.

The function by default returns the score in log2 following the package `Biostrings`.

### Value

a vector representing scores starting at each position, or a matrix with score in the two strands

### Examples

    if(require("PWMEnrich.Dmelanogaster.background")){
       data(MotifDb.Dmel)

       ttk = MotifDb.Dmel[["ttk"]]

       scanWithPWM(ttk, DNAString("CGTAGGATAAAGTAACT")) # odds average over the two strands expressed as log2-odds
       scanWithPWM(ttk, DNAString("CGTAGGATAAAGTAACT"), both.strands=TRUE) # log2-odds scores on both strands
    }

[Package PWMEnrich version 4.16.0 Index]