Thanks for these suggestions; I think they're worth considering. I've never been totally satisfied with (my function) flank(), because it's limited and its arguments are somewhat obscure in meaning. You can check out what we did in plyranges: https://rdrr.io/bioc/plyranges/man/flank-ranges.html. Your functions are more flexible, because they are two-way about the endpoint, like promoters(). Sometimes I've solved that with resize(flank()), but that's not ideal. 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. 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 wonder what Stuart Lee thinks?
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. Michael On Fri, Sep 13, 2019 at 4:48 AM Bhagwat, Aditya <aditya.bhag...@mpi-bn.mpg.de> wrote: > > Dear bioc-devel, > > The ?GenomicRanges::`intra-range-methods` are very useful for range > arithmetic<https://genomicsclass.github.io/book/pages/figure/bioc1_igranges-unnamed-chunk-6-1.png> > > Feedback request: would it be of general use to add the methods below to the > GenomicRanges::`intra-range-methods` palette (after properly S4-ing them)? > Or shall I keep them in > multicrispr<https://gitlab.gwdg.de/loosolab/software/multicrispr>? > Additional feedback welcome as well (e.g. re-implementation of already > existing functionality). > > > 1) Left flank > > #' Left flank > #' @param gr \code{\link[GenomicRanges]{GRanges-class}} > #' @param leftstart number: flank start (relative to range start) > #' @param leftend number: flank end (relative to range start) > #' @return a \code{\link[GenomicRanges]{GRanges-class}} > #' @export > #' @examples > #' bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr') > #' bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus > #' gr <- read_bed(bedfile, bsgenome) > #' left_flank(gr) > left_flank <- function(gr, leftstart = -200, leftend = -1){ > > # Assert > assert_is_identical_to_true(is(gr, 'GRanges')) > assert_is_a_number(leftstart) > assert_is_a_number(leftend) > > # Flank > newranges <- gr > end(newranges) <- start(gr) + leftend > start(newranges) <- start(gr) + leftstart > > # Return > newranges > } > > > 2) Right flank > > #' Right flank > #' @param gr \code{\link[GenomicRanges]{GRanges-class}} > #' @param rightstart number: flank start (relative to range end) > #' @param rightend number: flank end (relative to range end) > #' @return \code{\link[GenomicRanges]{GRanges-class}} > #' @export > #' @examples > #' bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr') > #' bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus > #' gr <- read_bed(bedfile, bsgenome) > #' right_flank(gr) > #' @export > right_flank <- function(gr, rightstart = 1, rightend = 200){ > > # Assert > assert_is_identical_to_true(is(gr, 'GRanges')) > assert_is_a_number(rightstart) > assert_is_a_number(rightend) > assert_is_a_bool(verbose) > > # Flank > newranges <- gr > start(newranges) <- end(newranges) + rightstart > end(newranges) <- end(newranges) + rightend > > # Plot > if (plot) plot_intervals(GRangesList(sites = gr, rightflanks = > newranges)) > > # Return > cmessage('\t\t%d right flanks : [end%s%d, end%s%d]', > length(newranges), > csign(rightstart), > abs(rightstart), > csign(rightend), > abs(rightend)) > newranges > } > > > 3) Slop > > #' Slop (i.e. extend left/right) > #' @param gr \code{\link[GenomicRanges]{GRanges-class}} > #' @param leftstart number: flank start (relative to range start) > #' @param rightend number: flank end (relative to range end) > #' @return \code{\link[GenomicRanges]{GRanges-class}} > #' @export > #' @examples > #' bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr') > #' bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus > #' gr <- read_bed(bedfile, bsgenome) > #' slop(gr) > #' @export > slop <- function(gr, leftstart = -22, rightend = 22){ > > # Assert > assert_is_identical_to_true(methods::is(gr, 'GRanges')) > assert_is_a_number(leftstart) > assert_is_a_number(rightend) > assert_is_a_bool(verbose) > > # Slop > newranges <- gr > start(newranges) <- start(newranges) + leftstart > end(newranges) <- end(newranges) + rightend > > # Return > newranges > } > > > 4) Flank fourways > > #' Flank fourways > #' > #' Flank left and right, for both strands, and merge overlaps > #' @param gr \code{\link[GenomicRanges]{GRanges-class}} > #' @param leftstart number: left flank start (relative to range start) > #' @param leftend number: left flank end (relative to range start) > #' @param rightstart number: right flank start (relative to range end) > #' @param rightend number: right flank end (relative to range end) > #' @return \code{\link[GenomicRanges]{GRanges-class}} > #' @examples > #' bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr') > #' bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus > #' granges <- read_bed(bedfile, bsgenome) > #' flank_fourways(granges) > #' @export > flank_fourways <- function(gr, leftstart = -200, leftend = -1, > rightstart = 1, rightend = 200){ > > # Comply > . <- NULL > > # Flank > left <- left_flank( gr, leftstart, leftend) > right <- right_flank(gr,rightstart, rightend) > newranges <- c(left, right) > > # Complement > newranges %<>% c(invertStrand(.)) > > # Merge overlaps > newranges %<>% reduce() # GenomicRanges::reduce > > # Return > newranges > } > > > > 5) Slop fourways > > #' Slop granges for both strands, merging overlaps > #' @param gr \code{\link[GenomicRanges]{GRanges-class}} > #' @param leftstart number > #' @param rightend number > #' @return \code{\link[GenomicRanges]{GRanges-class}} > #' @examples > #' bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr') > #' bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus > #' gr <- read_bed(bedfile, bsgenome) > #' gr > #' slop_fourways(gr) > #' @export > slop_fourways <- function(gr, leftstart = -22, rightend = 22){ > > # Comply > . <- NULL > > # Slop > if (verbose) cmessage('\tSlop fourways') > newranges <- slop(gr, leftstart, rightend, verbose = verbose) > > # Complement > newranges %<>% c(invertStrand(.)) > > # Merge overlaps > newranges %<>% reduce() > > # Return > newranges > } > > Thankyou! > > Aditya > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
