searchPairBSgenome-methods: searchPairBSgenome method

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

searchPairBSgenome method

Description

Given a chain file for liftover from one genome to another, it searches two BSgenome with a PWMatrix, and only reports the hits that are presents in two genomes with equivalent positions.

Usage

  searchPairBSgenome(pwm, BSgenome1, BSgenome2, chr1, chr2,
                     min.score="80%", strand="*", chain)

Arguments

pwm	A PWMatrix object or a PWMatrixList object.
BSgenome1, BSgenome2	A BSgenome class.
chr1, chr2	A character object, specifying the chromosomes you want to search.
min.score	The minimum score for the hit. Can be given an character string in th format of "80%" or as a single absolute value.
strand	When searching the alignment, we can search the positive "+" strand or negative "-" strand. While strand is "*", it will search both strands and return the results based on the positvie strand coordinate.
chain	A Chain object. It can be generated by import.chain from package rtracklayer. Please provide the chain from BSgenome1 to BSgenome2.

Value

A SitePairSet object is returned when pwm is a PWMatrix, while a SitePairSetList is returned when pwm is a PWMatrixList.

Author(s)

Ge Tan

See Also

searchAln

Examples

  ## Not run: 
    library(rtracklayer)
    library(JASPAR2014)
    library(BSgenome.Hsapiens.UCSC.hg19)
    library(BSgenome.Mmusculus.UCSC.mm10)
    data("MA0004.1")
    pfm <- MA0004.1
    pwm <- toPWM(pfm)
    chain <- import.chain("Downloads/hg19ToMm10.over.chain")
    sitepairset <- searchPairBSgenome(pwm, BSgenome.Hsapiens.UCSC.hg19,
                                      BSgenome.Mmusculus.UCSC.mm10,
                                      chr1="chr1", chr2="chr1",
                                      min.score="90%", strand="+", 
                                      chain=chain)
  
## End(Not run)

ge11232002/TFBSTools documentation built on June 12, 2025, 8:31 p.m.