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
