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al2na/getdata2.R

Last active August 14, 2016 10:10
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Raw
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)
Raw
hmap1.R
heatTargetAnnotation(peak2ann.l)
Raw
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)
Raw
install.genomation.R
# install the package from github
library(devtools)
install_github("BIMSBbioinfo/genomation",build_vignettes=FALSE)
Raw
peakAnn.R
peak2ann=annotateWithFeatures(p300,chrHMM.list)
peak2ann
Raw
peakAnn2.R
peak.list=GenomicRanges::GRangesList(p300=p300,SP1=SP1,NANOG=NANOG)
peak2ann.l=annotateWithFeatures(peak.list,chrHMM.list)
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