Hi, I observed this possibly unintended behavior of the score function in package IRanges: using 'score()<-' drops the rownames. Reproducible example. > rd1 = RangedData(ranges=IRanges(start=runif(4, min=1, max=10E8), width=runif(4, min=1, max=10E5), names=paste("bla",1:4)), space=1:2) > rownames(rd1) [1] "bla 1" "bla 3" "bla 2" "bla 4" > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-apple-darwin9.8.0 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_1.4.9 loaded via a namespace (and not attached): [1] tools_2.10.1 > > rd1 RangedData with 4 rows and 0 value columns across 2 spaces space ranges | <character> <iranges> | bla 1 1 [623833301, 624400493] | bla 3 1 [505448873, 505904729] | bla 2 2 [924959706, 925681728] | bla 4 2 [503293070, 504033700] | > rd1 RangedData with 4 rows and 1 value column across 2 spaces space ranges | score <character> <iranges> | <numeric> 1 1 [623833301, 624400493] | 0.2912978 2 1 [505448873, 505904729] | -0.5158529 3 2 [924959706, 925681728] | 0.7401251 4 2 [503293070, 504033700] | 1.1659967 > rownames(rd1) NULL

Michael, Thanks for the bug report! The issue was that the [[<-,RangedData method, which is called by score<-,RangedData, dropped row.names. This issue has been fixed in the BioC 2.5 IRanges (>= 1.4.15) and BioC 2.6 IRanges (>= 1.5.63) code lines and will be available at bioconductor.org within the next 36 hours. Patrick On 3/18/10 7:30 AM, Michael Dondrup wrote: > Hi, > I observed this possibly unintended behavior of the score function in package IRanges: > using 'score()<-' drops the rownames. > > Reproducible example. > >> rd1 = RangedData(ranges=IRanges(start=runif(4, min=1, max=10E8), width=runif(4, min=1, max=10E5), names=paste("bla",1:4)), space=1:2) >> rownames(rd1) >> > [1] "bla 1" "bla 3" "bla 2" "bla 4" > > >> sessionInfo() >> > R version 2.10.1 (2009-12-14) > x86_64-apple-darwin9.8.0 > > 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_1.4.9 > > loaded via a namespace (and not attached): > [1] tools_2.10.1 > >>> rd1 >>> > RangedData with 4 rows and 0 value columns across 2 spaces > space ranges | > <character> <iranges> | > bla 1 1 [623833301, 624400493] | > bla 3 1 [505448873, 505904729] | > bla 2 2 [924959706, 925681728] | > bla 4 2 [503293070, 504033700] | > >> rd1 >> > RangedData with 4 rows and 1 value column across 2 spaces > space ranges | score > <character> <iranges> |<numeric> > 1 1 [623833301, 624400493] | 0.2912978 > 2 1 [505448873, 505904729] | -0.5158529 > 3 2 [924959706, 925681728] | 0.7401251 > 4 2 [503293070, 504033700] | 1.1659967 > >> rownames(rd1) >> > NULL > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Sorry, I copy-pasted a bit chaotic, the (ir-)reproducible example should look like this: > rd1 = RangedData(ranges=IRanges(start=runif(4, min=1, max=10E8), width=runif(4, min=1, max=10E5), names=paste("bla",1:4)), space=1:2) > rd1 RangedData with 4 rows and 0 value columns across 2 spaces space ranges | <character> <iranges> | bla 1 1 [623833301, 624400493] | bla 3 1 [505448873, 505904729] | bla 2 2 [924959706, 925681728] | bla 4 2 [503293070, 504033700] | > rownames(rd1) [1] "bla 1" "bla 3" "bla 2" "bla 4" > score(rd1) = rnorm(4) > rd1 RangedData with 4 rows and 1 value column across 2 spaces space ranges | score <character> <iranges> | <numeric> 1 1 [623833301, 624400493] | 0.2912978 2 1 [505448873, 505904729] | -0.5158529 3 2 [924959706, 925681728] | 0.7401251 4 2 [503293070, 504033700] | 1.1659967 > rownames(rd1) NULL Am Mar 18, 2010 um 3:30 PM schrieb Michael Dondrup: > Hi, > I observed this possibly unintended behavior of the score function in package IRanges: > using 'score()<-' drops the rownames. > > Reproducible example. >> rd1 = RangedData(ranges=IRanges(start=runif(4, min=1, max=10E8), width=runif(4, min=1, max=10E5), names=paste("bla",1:4)), space=1:2) >> rownames(rd1) > [1] "bla 1" "bla 3" "bla 2" "bla 4" > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-apple-darwin9.8.0 > > 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_1.4.9 > > loaded via a namespace (and not attached): > [1] tools_2.10.1 >>> rd1 > RangedData with 4 rows and 0 value columns across 2 spaces > space ranges | > <character> <iranges> | > bla 1 1 [623833301, 624400493] | > bla 3 1 [505448873, 505904729] | > bla 2 2 [924959706, 925681728] | > bla 4 2 [503293070, 504033700] | >> rd1 > RangedData with 4 rows and 1 value column across 2 spaces > space ranges | score > <character> <iranges> | <numeric> > 1 1 [623833301, 624400493] | 0.2912978 > 2 1 [505448873, 505904729] | -0.5158529 > 3 2 [924959706, 925681728] | 0.7401251 > 4 2 [503293070, 504033700] | 1.1659967 >> rownames(rd1) > NULL > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor