wgEncodeTfbsV3 {ChIPpeakAnno} | R Documentation |
possible binding pool for human (hg19) from transcription factor binding site clusters (V3) from ENCODE data and removed the HOT spots
data("wgEncodeTfbsV3")
An object of GRanges.
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)
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/ wgEncodeRegTfbsClustered/wgEncodeRegTfbsClusteredV3.bed.gz
data(wgEncodeTfbsV3) head(wgEncodeTfbsV3)