HOT.spots: High Occupancy of Transcription Related Factors regions

Description

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

Usage

data("HOT.spots")

Arguments

format

An object of GRangesList

source

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

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)

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

Run this code

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

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