getdata2.R

p300.url="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescP300V0416102UniPk.narrowPeak.gz"

Nanog.url="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescNanogsc33759V0416102UniPk.narrowPeak.gz"

SP1.url="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/wgEncodeAwgTfbsHaibH1hescSp1Pcr1xUniPk.narrowPeak.gz"

chrHMM.url="http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmH1hescHMM.bed.gz"
#http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgSegmentation/wgEncodeAwgSegmentationChromhmmH1hesc.bed.gz"

# get chromHMM annotation and make a list out of it
library(genomation)
chrHMM=readBed(chrHMM.url)
chrHMM.list=GenomicRanges::split(chrHMM, chrHMM$name,drop=TRUE)

# get peaks
p300=readBed(p300.url)
SP1=readBed(SP1.url)
NANOG=readBed(Nanog.url)

hmap1.R

heatTargetAnnotation(peak2ann.l)

hmap2.R

mat=heatTargetAnnotation(peak2ann.l,plot=FALSE)
library(gplots)
heatmap.2(mat,col="topo.colors",cellnote=round(mat),
          notecol="black",trace="none",cexCol=0.5,cexRow=0.8)

install.genomation.R

# install the package from github
library(devtools)
install_github("BIMSBbioinfo/genomation",build_vignettes=FALSE)

peakAnn.R

peak2ann=annotateWithFeatures(p300,chrHMM.list)
peak2ann

peakAnn2.R

peak.list=GenomicRanges::GRangesList(p300=p300,SP1=SP1,NANOG=NANOG)
peak2ann.l=annotateWithFeatures(peak.list,chrHMM.list)