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Bioconductor / GenomicRanges

Representation and manipulation of genomic intervals
https://bioconductor.org/packages/GenomicRanges
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drop.self and drop.redundant for Genomic Ranges #71

Closed DarioS closed 1 year ago

DarioS commented 1 year ago

At the risk of reviving others' decade-old request, could the same options as for IRanges be supported for genomic ranges too?

hpages commented 1 year ago

With no context at all, it's impossible to know what you are talking about. What function? What decade-old request? What's your use case? What have you tried? MRE? sessionInfo()? Thank you

DarioS commented 1 year ago

Oh, I was referring to Janet Young's request of avoiding all of the self hits when there is only one input to findOverlaps. For IRanges, findOverlaps has ... which allows drop.self and drop.redundant but the GRanges variety does not have ellipsis and so it does not allow such parameters to be set by the end user. Worthwhile or not to harmonise?

hpages commented 1 year ago

This request from Janet Young is more than 8 years old. A few things happened in the meantime. Did you bother to try findOverlaps() on a GRanges object with drop.self=TRUE and/or drop.redundant=TRUE, and using a reasonably recent version of Bioconductor? If that doesn't work, then please reopen this issue and I apologize in advance.