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

In LihuaJulieZhu/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

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

Usage

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)

LihuaJulieZhu/ChIPpeakAnno documentation built on Aug. 5, 2020, 12:02 a.m.