It's on the right track. The case where two ranges are produced is problematic, because we would want this to be a parallel vector operation, where the length of the input is the same as the length of the output. So that last case I think might just ignore the leftend and rightstart arguments with a warning, returning a result with the gap filled.
Michael On Mon, Sep 16, 2019 at 1:48 AM Bhagwat, Aditya <aditya.bhag...@mpi-bn.mpg.de> wrote: > > Michael, actually, such a generic straddle() could be useful: > > straddle(leftstart=-100, rightend=100) # extended range > straddle(leftstart=-100, leftend=-1) # left flank > straddle(rightstart=1, rightend=100) # right flank > straddle(leftstart=-100, leftend=-1, rightstart=1, rightend=100) # left and > right flanks > > What do you think? > > 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 10:30 AM > To: Michael Lawrence > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods` > > 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 -- Michael Lawrence Scientist, Bioinformatics and Computational Biology Genentech, A Member of the Roche Group Office +1 (650) 225-7760 micha...@gene.com Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
