findOverlappingPeaks | peak取交集操作

 

参考：

• http://localhost:17449/lab/tree/projects/BAF_SOX9/diffbind/6.DMSO_only.ipynb
• http://localhost:17449/lab/tree/projects/BAF_SOX9/diffbind/2.2-Diffbind-Raghwan.ipynb#findOverlapsOfPeaks

 

venn图

options(repr.plot.width=5.5, repr.plot.height=5.5)
p <- ChIPpeakAnno::makeVennDiagram(list(#GRanges(subset(selected.norm.count, DMSO_SOX9_2_Paul>5)[,1:3]),
                                   GRanges(subset(selected.norm.count, dT29_SC1_DM1_Rag_b4>5)[,1:3]),
                                   GRanges(subset(selected.norm.count, dT29_ARD1_DM2_Rag_b4>5)[,1:3]),
                                   GRanges(subset(selected.norm.count, dT29_BRD9_DM1_Rag_b4>5)[,1:3]),
                                   GRanges(subset(selected.norm.count, dT29_PBR1_DM1_Rag_b4>5)[,1:3])
                                  ), 
                              NameOfPeaks=c("SMARCC1","ARID1","BRD9","PBR1"), minoverlap = 1, 
                scaled=FALSE, euler.d=FALSE, # totalTest=100, 
                fill=tmp.colors[2:5], # circle fill color
                col=tmp.colors[2:5] #circle border color
                # cat.col=c("#D55E00", "#0072B2")
                             )
p

　　

UpSetR图

require(UpSetR)
p1 <- upset(tmp.df, text.scale = 2, keep.order = T, intersections = tmp.intersections)

　　

findOverlapsOfPeaks取交集

t1 <- ChIPpeakAnno::findOverlapsOfPeaks(PBR1.peak.list$`4074 Loss`,
                                   PBR1.peak.list$`5758 Gain`,
                                   BRD9.peak.list$`4665 Loss`,
                                   BRD9.peak.list$`5755 Gain`)

　　

findOverlappingPeaks取交集【这个函数对两个set很友好，可以直接得到peak name】

peak.no.comp <- ChIPpeakAnno::findOverlappingPeaks(GRanges(norm.count[,1:3]), peak.list$`4074 Loss`)
peak.comp <- ChIPpeakAnno::findOverlappingPeaks(GRanges(norm.count[,1:3]), peak.list$`5758 Gain`)

peak.no.comp2 <- as.data.frame(peak.no.comp$Peaks1withOverlaps)
peak.comp2 <- as.data.frame(peak.comp$Peaks1withOverlaps)