TFBSTools (version 1.10.3)

searchPairBSgenome-methods: 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.

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)