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)
ao <- searchTFBPS(q, subj, motifs[["dist60"]], queryGenome=Hsapiens)

[Package enhancerHomologSearch version 0.99.17 Index]