MotifSet {TFBSTools} | R Documentation

## Class `"MotifSet"`

### Description

This MotifSet object is a container for storing the generated motifs from Motif identification softwares, such as MEME.

### Usage

      ## Constructor
      MotifSet(motifList=GRangesList(), motifEvalues=numeric(),
               subjectSeqs=DNAStringSet())

### Arguments

`motifList` | A GRangesList. Each GRanges store the starts, ends, strand, seqnames and scores information of one motif sites sequences.
`motifEvalues` | A numeric vector of the E values generated from MEME for each motif.
`subjectSeqs` | A DNAStringSet object. It stores the original sequences which are scanned by the software.

### Value

A `MotifSet` object is returned.

### Methods

[

  `signature(x = "MotifSet")`: Getter

consensusMatrix

  `signature(x = "MotifSet")`(x, as.prob = FALSE, shift = 0L, width = NULL, ...): Calculate the consensus matrix. Other arguments, please check the `consensusMatrix` in `Biostrings` package.

length

  `signature(x = "MotifSet")`: Returns the number of motifs.

sitesSeq

  `signature(x = "MotifSet")`(x, n=10L, type="none"): Gets the sites sequences.

  `n` is the number of bases to include from flanking region.

  `type` controls "all", "left", "right" or "none" flanking sequences are included.

### Author(s)

Ge Tan

### See Also

`runMEME`

### Examples

      ## Not run:
        motifSet <- runMEME(file.path(system.file("extdata", package="TFBSTools"),
                            "crp0.s"),
                            binary="/usr/local/Cellar/meme/4.10.1/bin/meme",
                            arguments=list("-nmotifs"=3))
        sitesSeq(motifSet, type="all")
        sitesSeq(motifSet, type="none")
        consensusMatrix(motifSet)

    ## End(Not run)

[Package TFBSTools version 1.18.0 Index]