HOT.spots: High Occupancy of Transcription Related Factors regions

Description Usage Format Details Source References Examples

Description

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

Usage

1

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

1
2
 data(HOT.spots)
 elementNROWS(HOT.spots)

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.