################ library(ChIPQC) load("/data/ChIPQC/ebf1_ChIPQCsample.RData") QCmetrics(exampleExp) ################ load("/data/ChIPQC/ebf1_FullyLoaded_ChIPQCsample.RData") QCmetrics(exampleExp) ################ plotCC(exampleExp) FragmentLengthCrossCoverage(exampleExp) RelativeCrossCoverage(exampleExp) ################ frip(exampleExp) plotFrip(exampleExp) plotFribl(exampleExp) ################ regi(exampleExp) plotRegi(exampleExp) ################ coveragehistogram(exampleExp)[1:10] sum(coveragehistogram(exampleExp)[-c(1:19)]) plotCoverageHist(exampleExp) ################ plotSSD(exampleExp) ################ ################ ################ load("/data/ChIPQC/SampleSheet.RData") SampleSheet[1:3,] #resExperiment = ChIPQC(SampleSheet,peaks=peaksFile,annotation="mm9",blacklist=BlackListFile) load("/data/ChIPQC/BCell_Examples.RData") QCmetrics(resExperiment)[5:10,] ################ FragmentLengthCrossCoverage(resExperiment)[1:3] RelativeCrossCoverage(resExperiment)[1:3] plotCC(resExperiment,colourBy="Tissue",facetBy="Factor",lineBy="Replicate") ################ ccplot <- plotCC(resExperiment,colourBy="Tissue",facetBy="Factor",lineBy="Replicate") ccplot +facet_wrap(~Factor,scales="free_y") ################ plotFrip(resExperiment) plotFribl(resExperiment) ################ plotRegi(resExperiment) regi(resExperiment)["All3utrs",] plotRegi(resExperiment)+scale_fill_gradient2(low="white",high="red", mid="white",midpoint=regi(resExperiment)["All3utrs","Input_Ch12"]) ################ plotCoverageHist(resExperiment,facetBy="Factor",colourBy="Tissue",lineBy="Replicate") ################ plotSSD(resExperiment) ################ plotCorHeatmap(resExperiment,facetBy="Factor") ################ ################ metrics <- QCmetrics(resExperiment) metricsMetadata <- data.frame(SampleID=rownames(metrics),RIP =metrics[,"RiP%",drop=T]) plotCC(resExperiment,addMetaData = metricsMetadata,colourBy="RIP") ################ metricsMetadata <- data.frame(SampleID=rownames(metrics),ChIPType= c(rep("Epigenetic Mark",1), rep("Transcription Factor",1), rep("Epigenetic Mark",4), rep("Transcription Factor",4), rep("Input",2), rep("Transcription Factor",1), rep("Epigenetic Mark",2), rep("Transcription Factor",2), rep("Epigenetic Mark",2))) plotSSD(resExperiment,addMetaData = metricsMetadata,facetBy="ChIPType") ################ DNAsePeaks <- peaks(QCsample(resExperiment,"DNAse")) H3K4me3Peaks <- peaks(QCsample(resExperiment,"H3K4me3_IkPos")) H3K9acPeaks <- peaks(QCsample(resExperiment,"H3K9ac_IkPos")) RNAPol2Peaks <- peaks(QCsample(resExperiment,"RNAPol2")) customAnnotation <- list(version="custom", DNAse=DNAsePeaks, RNAPol2=RNAPol2Peaks, H3K4me3=H3K4me3Peaks, H3K9ac=H3K9acPeaks) #bamFile <- "/data/ChIPQC/Chr11_Ebf1DupMarked.bam bamFile <- "/data/ChIPQC/Chr11_Ebf1DupMarked.bam" #exampleExpCA = ChIPQCsample(bamFile,peaks=NULL,annotation=customAnnotation,chromosomes="chr11") load("/data/ChIPQC/exampleCustomAnnotation.RData") plotRegi(exampleExpCA) ################ ccplot <- plotCC(resExperiment) ccplot$layers <- ccplot$layers[1] ccplot ################ plotFribl(resExperiment)+ylim(0,15) ################ plotCoverageHist(resExperiment)+xlim(0,250) ################ ################ ################ data(tamoxifen_QC) QCmetrics(tamoxifen) ## Some things to try plotCC(tamoxifen) plotCC(tamoxifen,colourBy="Tissue")+facet_wrap(~Factor,scales="free") plotFrip(tamoxifen) plotFribl(tamoxifen)+ylim(0,20) plotCoverageHist(tamoxifen)+xlim(0,1000) plotSSD(tamoxifen)+xlim(0,10)