################ 库(ChIPQC)加载(/数据/ ChIPQC / ebf1_ChIPQCsample.RData) QCmetrics (exampleExp ) ################ 负载(/数据/ 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]和(coveragehistogram (exampleExp) (- c (19))) plotCoverageHist (exampleExp ) ################ plotSSD (exampleExp ) ################ ################ ################负载(/数据/ ChIPQC / SampleSheet.RData) SampleSheet [1:3,] # resExperiment = ChIPQC (SampleSheet,山峰= peaksFile注释=“mm9”黑名单= BlackListFile)负载(/数据/ ChIPQC / BCell_Examples.RData) QCmetrics (resExperiment) [5:10 ,] ################ FragmentLengthCrossCoverage (resExperiment) [1:3] RelativeCrossCoverage (resExperiment) [1:3]plotCC (resExperiment colourBy = "组织",facetBy =“因素”,lineBy = "复制 ") ################ ccplot < - plotCC (resExperiment colourBy =“组织”,facetBy =“因素”,lineBy =“复制”)ccplot + facet_wrap(~因素,鳞片= " free_y ") ################ plotFrip resExperiment plotFribl (resExperiment ) ################ plotRegi (resExperiment)regi (resExperiment)(“All3utrs) plotRegi (resExperiment) + scale_fill_gradient2(低=“白色”,高=“红”,中期= "白",中点= regi (resExperiment)[“All3utrs”、“Input_Ch12 "]) ################ plotCoverageHist (resExperiment facetBy =“因素”,colourBy =“组织”,lineBy = "复制 ") ################ plotSSD (resExperiment ) ################ plotCorHeatmap (resExperiment facetBy =”因素 ") ################ ################ 指标< - QCmetrics (resExperiment)metricsMetadata < - data.frame (SampleID = rownames(指标),把=指标[,“把%”,放弃= T]) plotCC (resExperiment, addMetaData = metricsMetadata colourBy = " RIP ") ################ metricsMetadata < - data.frame (SampleID = rownames(指标),ChIPType = c(代表(“表观遗传标记”,1),代表(“转录因子”,1),代表(“表观遗传标记”,4),rep(“转录因子”，4)，rep(“输入”，2)，rep(“转录因子”，1)，rep(“表观遗传标记”，2)，rep(“转录因子”，2)，rep(“转录因子”，2)，代表(“表观遗传标记”,2)))plotSSD (resExperiment, addMetaData = metricsMetadata facetBy = " ChIPType ") ################ DNAsePeaks < -峰值(QCsample (resExperiment DNAse)) H3K4me3Peaks < -峰值(QCsample (resExperiment“H3K4me3_IkPos”))H3K9acPeaks < -峰值(QCsample (resExperiment“H3K9ac_IkPos”))RNAPol2Peaks < -峰值(QCsample (resExperiment RNAPol2 "))customAnnotation <- list(version="custom"， DNAse=DNAse peaks, RNAPol2=RNAPol2Peaks, H3K4me3=H3K4me3Peaks, H3K9ac=H3K9acPeaks) #bamFile <- "/data/ChIPQC/Chr11_Ebf1DupMarked. php . php . php . php . php。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)