[Bioc-devel] plyranges group_by

[Bhagwat, Aditya]

Hi Stuart, Michael,

Your plyranges package is really cool - now I am using it for left joining GRanges (I am facing a minor issue there<https://support.bioconductor.org/p/125623/>, but that is not the topic of this email - I have been asked by Lori not to double-post :-)).

This email is about the plyranges functionality for grouping GRanges.
That is cool, but I found it to be not so performant for large numbers of ranges.
My R session hangs when I do:

bedfile <- paste0('https://gitlab.gwdg.de/loosolab/software/multicrispr/wikis',
                      '/uploads/a51e98516c1e6b71441f5b5a5f741fa1/SRF.bed')
srfranges <- rtracklayer::import.bed(bedfile, genome = 'mm10')
txdb <- TxDb.Mmusculus.UCSC.mm10.ensGene::TxDb.Mmusculus.UCSC.mm10.ensGene
    generanges <- GenomicFeatures::genes(txdb)
annotatedsrf <- plyranges::join_overlap_left(srfranges, generanges)
plyranges::group_by(annotatedsrf, seqnames, start, end, strand)

For my purposes, I worked around it by performing a groupby in data.table:

data.table::as.data.table(annotatedsrf)[
    !is.na(gene_id),
    gene_id := paste0(gene_id, collapse = ';'),
    by = c('seqnames', 'start', 'end', 'strand'))

And was wondering, in general, whether it would be useful to have a data.table-based backend for plyranges::groupby()
And, whether all of this is actually a on-issue due to my improper use of plyranges::group_by properly.

Thank you for feebdack :-)

Aditya



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