Hi Aaron, Thanks for identifying this. I've updated the Ranges-utils.Rd file in the development branch and the change should be visible in 24-36 hours.
Valerie (new member of bioconductor team) On 08/26/2010 01:45 AM, Aaron Statham wrote: > Hi Patrick, > > Actually I'm happy with using ifelse() - could you update the > Ranges-utils.Rd (first hit for ?shift) as it currently says 'shift' must be > a single integer (but RangesList-utils.Rd is correct). > > Thanks, > Aaron > > On 26 August 2010 16:00, Patrick Aboyoun <[email protected]> wrote: > > >> Aaron, >> shift() currently doesn't respect strand because the most common use case >> for the function is to change from a 0-based index system to a 1-based index >> system, which is strand independent. The shift argument to the shift >> function, however, does accept an integer vector so you could use the >> following code, or something similar, to perform this operation somewhat >> efficiently: >> >> amount <- strand(g1) >> runValue(amount) <- ifelse(runValue(amount) == "-", -1L, 1L) >> shift(g1, as.vector(amount)) >> >> Perhaps this can be made simpler in the future if more users what >> strand-dependent shifting. >> >> >> Patrick >> >> >> >> >> On 8/25/10 9:54 PM, Aaron Statham wrote: >> >> >>> Hi all, >>> >>> Just ran into this - flank() takes notice of the strand for GRanges >>> objects, >>> whilst shift() doesn't. >>> Would it make sense for shift to use the strand in the GRanges method, or >>> is >>> there a nice alternative? (at the moment I'm doing a shift per strand) >>> >>> >>> g1<- GRanges(rep("chr1", 3), IRanges(rep(5, 3), width=1), c("+","-","*")) >>> >>>> g1 >>>> >>>> >>> GRanges with 3 ranges and 0 elementMetadata values >>> seqnames ranges strand | >>> <Rle> <IRanges> <Rle> | >>> [1] chr1 [5, 5] + | >>> [2] chr1 [5, 5] - | >>> [3] chr1 [5, 5] * | >>> >>> seqlengths >>> chr1 >>> NA >>> >>> >>>> flank(g1,3) >>>> >>>> >>> GRanges with 3 ranges and 0 elementMetadata values >>> seqnames ranges strand | >>> <Rle> <IRanges> <Rle> | >>> [1] chr1 [2, 4] + | >>> [2] chr1 [6, 8] - | >>> [3] chr1 [2, 4] * | >>> >>> seqlengths >>> chr1 >>> NA >>> >>> >>>> shift(g1,3) >>>> >>>> >>> GRanges with 3 ranges and 0 elementMetadata values >>> seqnames ranges strand | >>> <Rle> <IRanges> <Rle> | >>> [1] chr1 [8, 8] + | >>> [2] chr1 [8, 8] - | >>> [3] chr1 [8, 8] * | >>> >>> seqlengths >>> chr1 >>> NA >>> >>> R version 2.11.0 (2010-04-22) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 >>> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] GenomicRanges_1.0.7 IRanges_1.6.15 >>> >>> Thanks, >>> Aaron >>> >>> >>> >> > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
