Hmm no that wouldn't work, it would become messy trying to figure out when incompatible arguments are provided.
Aditya ________________________________________ From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Monday, September 16, 2019 10:09 AM To: Michael Lawrence Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods` Hi Michael, Thank you for the pointer to plyranges - looks very useful! > Maybe a better name is "straddle" for when ranges > straddle one of the endpoints? In keeping with the current pattern of > Ranges API, there would be a single function: straddle(x, side, left, > right, ignore.strand=FALSE). So straddle(x, "start", -100, 10) would > be like promoters(x, 100, 10) for a positive or "*" strand range. Cool suggestion, and a really fitting verb :-) Just slightly modifying your suggestion makes the API fully generic (waaw!), generalizing over left_flank, right_flank, as well as slop: straddle(leftstart, leftend, rightstart, rightend) Would it be worth having such functionality in GenomicRanges or plyranges, rather than multicrispr<https://gitlab.gwdg.de/loosolab/software/multicrispr>? > That brings up strandedness, which needs to be considered here. For > unstranded ranges, it may be that direct start() and end() > manipulation is actually more transparent than a special verb. I ended up using left/right for unstranded, and up/down for stranded operations. > The functions that involve reduce() wouldn't fit into the intrarange > operations, as they are summarizing ranges, not transforming them. > They may be going too far. True. Actually, the functions would be cleaner without the reduce(), I think I'll take that out. Cheers, Aditya [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
