searchPairBSgenome-methods {TFBSTools} | R Documentation |
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.
searchPairBSgenome(pwm, BSgenome1, BSgenome2, chr1, chr2, min.score="80%", strand="*", chain)
pwm |
A PWMatrix object or a PWMatrixList object. |
BSgenome1, BSgenome2 |
A |
chr1, chr2 |
A |
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 |
A SitePairSet
object is returned when pwm is a PWMatrix
,
while a SitePairSetList
is returned when pwm is a PWMatrixList
.
Ge Tan
## 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)