Description Usage Format Details Source Examples
possible binding pool for human (hg19) from transcription factor binding site clusters (V3) from ENCODE data and removed the HOT spots
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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
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