[BioC] IRanges: setting score() on RangedData drops rownames

Michael Dondrup Michael.Dondrup at uni.no
Thu Mar 18 15:30:50 CET 2010


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



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