prepareBindingSitesList {ATACseqQC}R Documentation

helper function for preparing the binding list

Description

helper function for preparing the binding list

Usage

prepareBindingSitesList(pfms, genome, seqlev = paste0("chr", c(1:22, "X",
  "Y")), expSiteNum = 5000)

Arguments

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.

Examples

library(MotifDb)
motifs <- query(MotifDb, c("Hsapiens"))
motifs <- as.list(motifs)
library(BSgenome.Hsapiens.UCSC.hg19)
#bindingSitesList <- prepareBindingSitesList(motifs, genome=Hsapiens)

[Package ATACseqQC version 1.6.4 Index]