[Bioc-devel] Extending GenomicRanges::`intra-range-methods`
Michael Lawrence
|@wrence@m|ch@e| @end|ng |rom gene@com
Fri Sep 13 14:38:37 CEST 2019
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.Bhagwat using 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]]
>
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--
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
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