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LTLA / InteractionSet

Clone of the Bioconductor repository for the InteractionSet package, see https://bioconductor.org/packages/devel/bioc/html/InteractionSet.html for the official development version.
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GInteraction from Pairwise interaction bed? #2

Closed rdali closed 6 years ago

rdali commented 6 years ago

Hello, I have Pairwise interaction beds in the following format: baitChr baitStart baitEnd otherEndChr otherEndStart otherEndEnd score chr1 927395 936954 chr1 850619 874081 5.16 chr1 927395 936954 chr1 1109733 1122642 5.36 chr1 1239426 1278099 chr1 1206874 1212438 5.10 chr1 1545983 1552729 chr1 1585572 1619752 5.86 chr1 1585572 1619752 chr1 1647157 1648710 9.45

I am wondering if there is a function that turns this format into a GInteractions object. I could create GRanges from the first 3 lines and GRanges from lines 4-6 and use "GInteractions(region.1, region.2)" but then I would loose the interaction score which I would like to keep. Breaking it down seems tedious since Pairwise interaction beds have become more common.

Thank you! Rola

rdali commented 6 years ago

I realized there was a closed issue with a similar question. I had to reformat my file to a traditional bedpe format and used:

mybedpe<- rtracklayer::import("myfile", format = "bedpe") mybedpe.gi <- makeGInteractionsFromGRangesPairs(mybedpe)