searchTFBPS: Transcription Factor Binding Pattern Similarity (TFBPS)...

In jianhong/enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer

Transcription Factor Binding Pattern Similarity (TFBPS) search

Description

Search the TFBPs for query in subject.

Usage

searchTFBPS(
  query,
  subject,
  PWMs,
  queryGenome,
  background = "genome",
  ...,
  maximalShuffleEnhancers = 1000
)

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'.
maximalShuffleEnhancers	The maximal number of Shuffled enhancers. If the number of the input enhancer candidates is greater than maximalShuffleEnhancers, no shuffled enhancer sequences will be included. The shuffled enhancers will be created by shuffle.

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,
                  maximalShuffleEnhancers = 50)

jianhong/enhancerHomologSearch documentation built on Nov. 4, 2024, 8:29 p.m.