R/HOT.spots.R

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

#' High Occupancy of Transcription Related Factors regions
#' 
#' High Occupancy of Transcription Related Factors regions of human (hg19)
#' 
#' 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)
#' 
#' @name HOT.spots
#' @docType data
#' @format An object of GRangesList
#' @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.
#' @source http://metatracks.encodenets.gersteinlab.org/
#' @keywords datasets
#' @examples
#' 
#'  data(HOT.spots)
#'  elementNROWS(HOT.spots)
#' 
"HOT.spots"