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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel