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ComputationalRegulatoryGenomicsICL / GenomicInteractions

R/Bioconductor package for handling Genomic interaction data, annotating genomic features with interaction information and producing summary plots / statistics
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degree overlap annotateInteractions() #16

Open jaclyn-marie opened 1 year ago

jaclyn-marie commented 1 year ago

Hello Again,

I have a question regarding annotateInteractions().

When I use this tool to annotate anchors (ie promoters, enhancers), I end up getting a lot of anchors classified as "distal" if a feature does not 100% overlap with the anchor. I was wondering if there is a way to set a minimum degree/bp overlap to qualify features for annotation. Thanks for taking the time!

Sincerely, Jaclyn

liz-is commented 1 year ago

Hi (sorry for the slow reply, I was away at a conference), This shouldn't happen - could you provide a reproducible example with one or two interactions and example regions so that I can see how to fix this? Thanks!

jaclyn-marie commented 1 year ago

Hi @liz-is,

This was an error on my part, my apologies. I had been meaning to take this down before you replied. However, is the minimum overlap for this function set to 1 nt/bp? I was going to make some simple files to check the degree of overlap, but I have not yet done this.

J

liz-is commented 1 year ago

It's just using the default parameters for GenomicRanges::findOverlaps(), so yes. Probably the function should take additional arguments that are passed on to findOverlaps to control this, though. I'll see if I have time to implement this - or feel free to have a go at this yourself and send a pull request, if you like! :)