HOT.spots: High Occupancy of Transcription Related Factors regions

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

High Occupancy of Transcription Related Factors regions

Description

High Occupancy of Transcription Related Factors regions of human (hg19)

Usage

HOT.spots

Format

An object of GRangesList

Details

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)

Source

http://metatracks.encodenets.gersteinlab.org/

References

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.

Examples

 data(HOT.spots)
 elementNROWS(HOT.spots)

jianhong/ChIPpeakAnno documentation built on Feb. 2, 2024, 3:26 p.m.