On Thu, Feb 24, 2011 at 7:41 AM, Ivan Gregoretti <[email protected]> wrote:
> Hi Michael and Janet, > > I think that the reduce bug still persists in the devel branch. I > updated all my Bioconductor packages yesterday and yet, following her > steps I get > reduce(myregions_RD) > Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism > > I hope the sessionInfo() helps. > > Think this needs 1.9.25. Should be out tomorrow. Thanks, Michael > Thank you, > > Ivan > > > sessionInfo() > R version 2.13.0 Under development (unstable) (2010-12-02 r53747) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ChIPpeakAnno_1.7.0 limma_3.7.23 > [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 > [5] RSQLite_0.9-4 DBI_0.2-5 > [7] AnnotationDbi_1.13.13 > BSgenome.Ecoli.NCBI.20080805_1.3.17 > [9] multtest_2.7.1 Biobase_2.11.8 > [11] biomaRt_2.7.1 BSgenome.Mmusculus.UCSC.mm9_1.3.17 > [13] BSgenome_1.19.3 Biostrings_2.19.9 > [15] GenomicRanges_1.3.18 IRanges_1.9.22 > > loaded via a namespace (and not attached): > [1] MASS_7.3-11 RCurl_1.5-0 splines_2.13.0 survival_2.36-5 > [5] XML_3.2-0 > > > Ivan Gregoretti, PhD > National Institute of Diabetes and Digestive and Kidney Diseases > National Institutes of Health > 5 Memorial Dr, Building 5, Room 205. > Bethesda, MD 20892. USA. > Phone: 1-301-496-1016 and 1-301-496-1592 > Fax: 1-301-496-9878 > > > > On Thu, Feb 24, 2011 at 9:46 AM, Michael Lawrence > <[email protected]> wrote: > > Thanks. Seems to be fixed already in devel. > > > > On Wed, Feb 23, 2011 at 12:15 PM, Janet Young <[email protected]> wrote: > > > >> Hi again, > >> > >> I noticed that "reduce" gives an error on RangedData objects if there > are > >> space names that contain no ranges: > >> Error in endoapply(x[, by], FUN) : 'FUN' did not produce an > >> endomorphism > >> > >> I can work around it, but it'd great not to need to do that. All the > >> details are below. > >> > >> thanks very much, > >> > >> Janet > >> > >> ------------------------------------------------------------------- > >> > >> Dr. Janet Young (Trask lab) > >> > >> Fred Hutchinson Cancer Research Center > >> 1100 Fairview Avenue N., C3-168, > >> P.O. Box 19024, Seattle, WA 98109-1024, USA. > >> > >> tel: (206) 667 1471 fax: (206) 667 6524 > >> email: jayoung ...at... fhcrc.org > >> > >> http://www.fhcrc.org/labs/trask/ > >> > >> ------------------------------------------------------------------- > >> > >> > >> > >> > library(IRanges,warn.conflicts=F) > >> > >> > myregions_RD <- > >> > RangedData(IRanges(start=c(101L,201L,101L,101L),end=c(250L,300L,220L,501L)),space=c("chr1","chr1","chr1","chr2"),strand=c("+","+","+","+") > >> ) > >> > >> > #### this works > >> > reduce(myregions_RD) > >> RangedData with 2 rows and 1 value column across 2 spaces > >> space ranges | strand > >> <character> <IRanges> | <character> > >> 1 chr1 [101, 300] | + > >> 2 chr2 [101, 501] | + > >> > >> > ### drop regions that are bigger than 300bp (now there's nothing left > on > >> chr2) > >> > myregions_RD <- myregions_RD[which(width(myregions_RD)<=300),] > >> > >> > ### this doesn't work - reduce doesn't like a space without any > elements > >> > reduce(myregions_RD) > >> Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism > >> > >> > ### workaround - drop the unused space names > >> > myregions_RD <- > >> > RangedData(IRanges(start=start(myregions_RD),end=end(myregions_RD)),space=as.character(space(myregions_RD)),strand=myregions_RD$strand > >> ) > >> > >> > ### now it works > >> > reduce(myregions_RD) > >> RangedData with 1 row and 1 value column across 1 space > >> space ranges | strand > >> <character> <IRanges> | <character> > >> 1 chr1 [101, 300] | + > >> > >> > sessionInfo() > >> R version 2.12.1 (2010-12-16) > >> Platform: i386-apple-darwin9.8.0/i386 (32-bit) > >> > >> locale: > >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] IRanges_1.8.9 > >> > >> _______________________________________________ > >> Bioc-sig-sequencing mailing list > >> [email protected] > >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
