Differences between bedtools overlap / findOverlaps and findOverlapsOfPeaks about chippeakanno HOT 10 OPEN

@csijcs Thank you for trying ChIPpeakAnno to annotate your data. I have trouble in understanding your question. Could you please show me the sample to explain your question? Here may be something you want read: https://bioconductor.org/packages/release/bioc/vignettes/ChIPpeakAnno/inst/doc/FAQs.html#Find_Overlaps_of_Peaks

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Intersecting with bedtools:
$ bedtools intersect -a file1.bed -b file2.bed | wc -l
1962

Using findOverlaps:
> findOverlaps(file1,file2)
Hits object with 1962 hits and 0 metadata columns:

Using findOverlapsOfPeaks:
> findOverlapsOfPeaks(file1,file2)$venn_cnt[4,3]
Counts
1956

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Could you share the image by following codes:

ol <- findOverlapsOfPeaks(file1,file2, connectedPeaks='keepAll')
makeVennDiagram(ol)

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test.pdf

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sorry,
I forget the parameters for venndiagram
makeVennDiagram(ol, connectedPeaks='keepAll')

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test.pdf

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now try to run

ol <- findOverlaps(file1,file2)
length(unique(queryHits(ol)))
length(unique(subjectHits(ol)))

and share me the number

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> length(unique(queryHits(ol)))
[1] 1961
> length(unique(subjectHits(ol)))
[1] 1957

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I think you figure it out the difference. Let me know if you still have any questions.

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Got it, thanks!

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