Hi all, Are there any plans to add import/export support for the BEDPE format in rtracklayer? http://bedtools.readthedocs.org/en/latest/content/general-usage.html#bedpe-format I'd imagine that a hypothetical import method would return a GRangesList of length equal to the number of rows, where each internal GRanges has two entries representing the paired regions for the corresponding row. Extra interaction-specific metadata fields (e.g., score, user-defined fields) could be stuffed into the GRangesList's elementMetadata slot. The same object would also be used for export to the BEDPE format. This functionality would be useful for people working on structural variations, genomic interactions, etc. for which BEDPE is often used. The GenomicInteractions package has already got something for this, but it seems like rtracklayer would be a better (i.e., more general) home for that kind of function. If anyone's interested, we (i.e., Malcolm and Liz, the GenomicInteractions developers) would be willing to help migrate it over. Cheers, Aaron (+ Malcolm and Liz)
[Bioc-devel] support for BEDPE import/export in rtracklayer?
2 messages · Aaron Lun, Michael Lawrence
It's a shame that the format violates the BEDX+Y convention by inserting the second chr, start and end before some of the canonical BED fields. Anyway, I think it would be great if you guys could contribute a parser. Maybe just fork the github mirror? Michael
On Tue, Dec 8, 2015 at 1:24 PM, Aaron Lun <alun at wehi.edu.au> wrote:
Hi all, Are there any plans to add import/export support for the BEDPE format in rtracklayer? http://bedtools.readthedocs.org/en/latest/content/general-usage.html#bedpe-format I'd imagine that a hypothetical import method would return a GRangesList of length equal to the number of rows, where each internal GRanges has two entries representing the paired regions for the corresponding row. Extra interaction-specific metadata fields (e.g., score, user-defined fields) could be stuffed into the GRangesList's elementMetadata slot. The same object would also be used for export to the BEDPE format. This functionality would be useful for people working on structural variations, genomic interactions, etc. for which BEDPE is often used. The GenomicInteractions package has already got something for this, but it seems like rtracklayer would be a better (i.e., more general) home for that kind of function. If anyone's interested, we (i.e., Malcolm and Liz, the GenomicInteractions developers) would be willing to help migrate it over. Cheers, Aaron (+ Malcolm and Liz)
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel