prepareBindingSitesList {ATACseqQC} | R Documentation |
helper function for preparing the binding list
prepareBindingSitesList(pfms, genome, seqlev = paste0("chr", c(1:22, "X", "Y")), expSiteNum = 5000)
pfms |
A list of Position frequency Matrix represented as a numeric matrix with row names A, C, G and T. |
genome |
An object of BSgenome. |
seqlev |
A vector of characters indicates the sequence levels. |
expSiteNum |
numeric(1). Expect number of predicted binding sites. if predicted binding sites is more than this number, top expSiteNum binding sites will be used. |
library(MotifDb) motifs <- query(MotifDb, c("Hsapiens")) motifs <- as.list(motifs) library(BSgenome.Hsapiens.UCSC.hg19) #bindingSitesList <- prepareBindingSitesList(motifs, genome=Hsapiens)