wgEncodeTfbsV3 {ChIPpeakAnno}R Documentation

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")

Format

An object of GRanges.

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)

Source

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

Examples

data(wgEncodeTfbsV3)
head(wgEncodeTfbsV3)

[Package ChIPpeakAnno version 3.18.1 Index]