searchTFBPS {enhancerHomologSearch} | R Documentation

## Transcription Factor Binding Pattern Similarity (TFBPS) search

### Description

Search the TFBPs for query in subject.

### Usage

    searchTFBPS(query, subject, PWMs, queryGenome, background = "genome", ...)

### Arguments

`query` | An object of DNAStringSet to represent enhancer
`subject` | Output of getENCODEdata. An object of Enhancers
`PWMs` | The Position Weight Matrix list represented as a numeric matrix. Object of PWMatrixList or PFMatrixList.
`queryGenome` | An object of BSgenome for query data.
`background` | background nucleotide frequencies. Default is "genome". Refer matchMotifs for details.
`...` | Parameters will be passed to matchMotifs except 'out' and 'genome'.

### Value

An object of Enhancers.

### Examples

    library(BSgenome.Hsapiens.UCSC.hg38)
    peaks <- GRanges("chr1", IRanges(seq(5000, 50000, by=1000), width=1000))
    peaks$id <- paste(seq_along(peaks), 1, sep="_")
    subj <- Enhancers(genome=Hsapiens, peaks=peaks)
    q <- getSeq(Hsapiens, GRanges("chr1", IRanges(90000, width=1000)))
    data(motifs)
    if(.Platform$OS.type!="windows"){
      ao <- searchTFBPS(q, subj, motifs[["dist60"]], queryGenome=Hsapiens)
    }

[Package enhancerHomologSearch version 1.0.1 Index]