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step6-ChIPpeakAnno-Venn.R

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step6-ChIPpeakAnno-Venn.R

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rm(list=ls())

require(ChIPseeker)

require(TxDb.Hsapiens.UCSC.hg19.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

require(clusterProfiler)

bedFiles=list.files(pattern = '*bed')

library(ChIPpeakAnno)

BAF180_CT10_peaks <- readPeakFile( bedFiles[1] )

BAF180_CT22_peaks <- readPeakFile( bedFiles[2] )

BAF180_CT22AM_peaks <- readPeakFile( bedFiles[3] )

SRC2mutREV_ERB_peaks <- readPeakFile( bedFiles[4] )

WT_REV_ERB_peaks <- readPeakFile( bedFiles[5] )

ol <- findOverlapsOfPeaks(BAF180_CT10_peaks, BAF180_CT22_peaks,BAF180_CT22AM_peaks,

SRC2mutREV_ERB_peaks,WT_REV_ERB_peaks)

png('overlapVenn.png')

makeVennDiagram(ol)

dev.off()

BAF180_ol <- findOverlapsOfPeaks(BAF180_CT10_peaks, BAF180_CT22_peaks,BAF180_CT22AM_peaks )

png('BAF180_overlapVenn.png')

makeVennDiagram(BAF180_ol)

dev.off()

SRC2_ol <- findOverlapsOfPeaks( SRC2mutREV_ERB_peaks,WT_REV_ERB_peaks)

png('SRC2_overlapVenn.png')

makeVennDiagram(SRC2_ol)

dev.off()