motifScores {PWMEnrich} | R Documentation

## Motif affinity or number of hits over a threshold

### Description

Scan a number of sequences either to find overall affinity, or a number of hits over a score threshold.

### Usage

    motifScores(
      sequences,
      motifs,
      raw.scores = FALSE,
      verbose = TRUE,
      cutoff = NULL
    )

### Arguments

`sequences` | a set of sequences to be scanned, a list of DNAString or other scannable objects
`motifs` | a list of motifs either as frequency matrices (PFM) or as PWM objects. If PFMs are specified they are converted to PWMs using uniform background.
`raw.scores` | if to return raw scores (odds) for each position in the sequence. Note that scores for forward and reverse strand are concatenated into a single long vector of scores (twice the length of the sequence)
`verbose` | if to print verbose output
`cutoff` | if not NULL, will count number of matches with score above value specified (instead of returning the average affinity). Can either be one value, or a vector of values for each of the motifs.

### Value

if raw.scores=FALSE, returns a matrix of mean scores (after cutoff if any), where columns are motifs. The returned values are either mean odd scores (not log-odd), or number of hits above a threshold; otherwise if raw.scores=TRUE, returns a list of raw score values (before cutoff)

### Examples

    if(requireNamespace("PWMEnrich.Dmelanogaster.background")){
       data(MotifDb.Dmel, package = "PWMEnrich.Dmelanogaster.background")

       # affinity scores
       affinity = motifScores(DNAString("CGTAGGATAAAGTAACTAGTTGATGATGAAAG"), MotifDb.Dmel)

       # motif hit count with Patser score of 4
       counts = motifScores(DNAString("CGTAGGATAAAGTAACTAGTTGATGATGAAAG"), MotifDb.Dmel,
         cutoff=log2(exp(4)))

       print(affinity)
       print(counts)

       # scanning multiple sequences
       sequences = list(DNAString("CGTAGGATAAAGTAACTAGTTGATGATGAAAG"),
         DNAString("TGAGACGAAGGGGATGAGATGCGGAAGAGTGAAA"))
       affinity2 = motifScores(sequences, MotifDb.Dmel)
       print(affinity2)
    }

[Package PWMEnrich version 4.28.1 Index]