Description Usage Arguments Value Author(s) See Also Examples
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.
1 2 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
|
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