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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/HOT.spots.Rd_%03d_medium.png", width=480, height=480)
> ### Name: HOT.spots
> ### Title: High Occupancy of Transcription Related Factors regions
> ### Aliases: HOT.spots
> ### Keywords: datasets
> 
> ### ** Examples
> 
>  data(HOT.spots)
>  elementNROWS(HOT.spots)
    HOT_distal_Gm12878      HOT_distal_H1hesc      HOT_distal_Helas3 
                 21465                  27212                  25733 
      HOT_distal_Hepg2        HOT_distal_K562            HOT_Gm12878 
                 25402                  17944                  92592 
            HOT_H1hesc             HOT_Helas3              HOT_Hepg2 
                105036                  95054                  95998 
HOT_intergenic_Gm12878  HOT_intergenic_H1hesc  HOT_intergenic_Helas3 
                 21465                  27212                  25733 
  HOT_intergenic_Hepg2    HOT_intergenic_K562               HOT_K562 
                 25402                  17944                  81436 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>