searchTFBPS {enhancerHomologSearch} | R Documentation |
Search the TFBPs for query in subject.
searchTFBPS(query, subject, PWMs, queryGenome, background = "genome", ...)
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'. |
An object of Enhancers.
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)