Comments (10)
@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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from chippeakanno.
sorry,
I forget the parameters for venndiagram
makeVennDiagram(ol, connectedPeaks='keepAll')
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from chippeakanno.
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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Related Issues (20)
- invalid class "CompressedGRangesList" object HOT 1
- genomicElementDistribution not found HOT 5
- Error with `bindingType` in `annotatePeakInBatch` HOT 2
- toGRanges() no longer working in response to UCSC update HOT 3
- Questions on the how genomicElementDistribution works HOT 1
- error in enrichmentPlot() when providing a partially empty GO object HOT 1
- toGRanges() can't read in file name HOT 1
- disjointExons removed in Bioconductor 3.17 HOT 1
- How to understand otherExon HOT 7
- `findOverlapsOfPeaks(gr1, gr2)` Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs. HOT 6
- How to set the circle size same proportion of the number of peaks when there are more than 2 sets using `makeVennDiagram`? HOT 5
- oligoSummary not populating the motif matrix output field HOT 2
- makeVennDiagram fails with error 'Unexpected parameter length for "col"' HOT 4
- cvglists rtracklayer import error: Error in stop_if_wrong_length(what, ans_len) 'ranges' must have the length of the object to construct HOT 4
- hello,I don't know how to deal with it,can you help me figure it out. thanks HOT 8
- makeVennDiagram produces undesired console output HOT 6
- Regarding oligoSummary() HOT 1
- Annotation for dm6 does not contain gene_name HOT 2
- save featureAlignedHeatmap output to picture file ? HOT 2
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