MotifSet-class: Class '"MotifSet"'

In ge11232002/TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

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)  

ge11232002/TFBSTools documentation built on Dec. 26, 2024, 12:38 a.m.