searchPairBSgenome-methods {TFBSTools} | R Documentation

## 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)

[Package TFBSTools version 1.28.0 Index]