SiteSet-class: Class '"SiteSet"'

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

Description

The SiteSet object is a container for storing a set of putative transcription factor binding sites on a nucleotide sequence (start, end, strand, score, pattern as a PWMatrix, etc.)

Usage

## Constructors:
SiteSet(views, score, strand="*", seqname="Unknown", sitesource="TFBS", 
        primary="TF binding site", pattern)

Arguments

views	Object of class "XStringViews": It holds the start, end and the nucleotide sequence information of the transcription factor binding sites.
score	Object of class "numeric": A vector of PWM score for each putative binding site based on the PWM matrix..
strand	Object of class "character": The binding site is from the positive ("+"), negative ("-") or unknown("*") strand.
seqname	Object of class "character": The seqname of the sequence which contains these binding sites.
sitesource	Object of class "character": Currently it is set to "TFBS"
primary	Object of class "character": Currently it is set to "TF binding site"
pattern	Object of class "PWMatrix": The PWMatrix object which is used to search the binding sites.

Details

The score retuned in SiteSet is the absolute score of each putative TFBS scanned by the corresponding PWM. The way of calculating the score is shown on the refernce, Page 281.

Methods

[

signature(x = "SiteSet"): Getter function.

length

signature(x = "SiteSet"): The number of binding sites in this SiteSet.

pattern

signature(x = "SiteSet"): Returns the PWMatrix used.

relScore

signature(x = "SiteSet"): Gets relative score (between 0.0 to 1.0) with respect of the score range of the associated pattern (PWMatrix).

score

signature(x = "SiteSet"): Returns the score of each site.

seqname

signature(x = "SiteSet"): Returns the sequence name of the sequence which contains these sites.

strand

signature(x = "SiteSet"): Returns the strand information.

views

signature(x = "SiteSet"): Returns the views object.

start

signature(x = "SiteSet"): Returns the start coordinates.

end

signature(x = "SiteSet"): Returns the end coordinates.

pvalues

signature(x = "SiteSet") (x, type=c("TFMPvalue", "sampling")): Calculates the empirical p-values for the scores with two methods: the exact method from TFMPaluve package or implementation of sampling in this package. The background probability for sampling is based on the PWM matrix in the SiteSet object.

Author(s)

Ge Tan

References

Wasserman, W. W., & Sandelin, A. (2004). Applied bioinformatics for the identification of regulatory elements. Nature Publishing Group, 5(4), 276-287. doi:10.1038/nrg1315

See Also

searchSeq, searchAln, PWMatrix, SiteSetList, SitePairSet

Examples

    data(MA0003.2)
    pwm <- toPWM(MA0003.2)
    siteset <- searchSeq(pwm, "GAATTCTCTCTTGTTGTAGTCTCTTGACAAAATG", 
                         min.score="60%")
    writeGFF3(siteset, scoreType="absolute")
    as(siteset, "data.frame")
    as(siteset, "DataFrame")
    as(siteset, "GRanges")
    
    relScore(siteset)
    pvalues(siteset, type="TFMPvalue")
    pvalues(siteset, type="sampling")

TFBSTools documentation built on Nov. 8, 2020, 8:14 p.m.