wgEncodeTfbsV3: transcription factor binding site clusters (V3) from ENCODE

Description

possible binding pool for human (hg19) from transcription factor binding site clusters (V3) from ENCODE data and removed the HOT spots

Usage

data("wgEncodeTfbsV3")

Arguments

format

An object of GRanges.

source

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/ wgEncodeRegTfbsClustered/wgEncodeRegTfbsClusteredV3.bed.gz

Details

How to generate the data: temp <- tempfile() download.file(file.path("http://hgdownload.cse.ucsc.edu", "goldenPath", "hg19", "encodeDCC", "wgEncodeRegTfbsClustered", "wgEncodeRegTfbsClusteredV3.bed.gz"), temp) data <- read.delim(gzfile(temp, "r"), header=FALSE) unlink(temp) colnames(data)[1:4] <- c("seqnames", "start", "end", "TF") wgEncodeRegTfbsClusteredV3 <- GRanges(as.character(data$seqnames), IRanges(data$start, data$end), TF=data$TF) data(HOT.spots) hot <- reduce(unlist(HOT.spots)) ol <- findOverlaps(wgEncodeRegTfbsClusteredV3, hot) wgEncodeTfbsV3 <- wgEncodeRegTfbsClusteredV3[-unique(queryHits(ol))] wgEncodeTfbsV3 <- reduce(wgEncodeTfbsV3) save(list="wgEncodeTfbsV3", file="data/wgEncodeTfbsV3.rda", compress="xz", compression_level=9)

Examples

Run this code

data(wgEncodeTfbsV3)
head(wgEncodeTfbsV3)

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