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")
Format
An object of GRanges.Source
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/
wgEncodeRegTfbsClustered/wgEncodeRegTfbsClusteredV3.bed.gzDetails
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 codedata(wgEncodeTfbsV3)
head(wgEncodeTfbsV3)
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