HOT.spots {ChIPpeakAnno} | R Documentation

## High Occupancy of Transcription Related Factors regions

### Description

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

### Usage

    data("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)

[Package ChIPpeakAnno version 3.12.7 Index]