Description Usage Format Details Source References Examples
High Occupancy of Transcription Related Factors regions of human (hg19)
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An object of GRangesList
How to generated the data:
temp <- tempfile()
url <- "http://metatracks.encodenets.gersteinlab.org"
download.file(file.path(url, "HOT_All_merged.tar.gz"), temp)
temp2 <- tempfile()
download.file(file.path(url, "HOT_intergenic_All_merged.tar.gz"), temp2)
untar(temp, exdir=dirname(temp))
untar(temp2, exdir=dirname(temp))
f <- dir(dirname(temp), "bed$")
HOT.spots <- sapply(file.path(dirname(temp), f), toGRanges, format="BED")
names(HOT.spots) <- gsub("_merged.bed", "", f)
HOT.spots <- sapply(HOT.spots, unname)
HOT.spots <- GRangesList(HOT.spots)
save(list="HOT.spots",
file="data/HOT.spots.rda",
compress="xz", compression_level=9)
http://metatracks.encodenets.gersteinlab.org/
Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012 Sep 26;13(9):R48. doi: 10.1186/gb-2012-13-9-r48. PubMed PMID: 22950945; PubMed Central PMCID: PMC3491392.
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