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jianhong / ChIPpeakAnno

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Number of Overlap Peaks #44

Open zhangqc723 opened 2 weeks ago

zhangqc723 commented 2 weeks ago

Dear Now, I want to get the overlap of three peak sets and I run followed code in R _ol <- findOverlapsOfPeaks(CnT_WT_Rep1, CnT_WT_Rep2, CnT_WTRep3, connectedPeaks = "keepAll") _dat1 <- ol[["peaklist"]][["CnT_WT_Rep1///CnT_WT_Rep2///CnT_WTRep3"]] %>% as.data.frame() And I get a peaks set with 831 lines, but the Venn plot show 837, Could you tell me how to fix it? Thanks!

Venn plot code : makeVennDiagram(ol, NameOfPeaks = c('df1','df2','df3'), fill=c("#CC79A7", "#56B4E9",'#0072B2'), connectedPeaks = "keepAll")

image

jianhong commented 2 weeks ago

Hi,

Thank you for trying ChIPpeakAnno to annotate your data. This is a little bit hard to understand the number. The output lines is the merged overlaps. It should be no greater than the number of overlaps. Think about the situation for multiple continuous peaks for different samples merged together. Try to change the connectedPeaks to 'merge' to see if the number will be fixed.