[BioC] Adding names to a IRanges object

[Patrick Aboyoun]

Daniel,
IRanges objects do support names and they can be added using the 
"names<-" replacement function.

 > suppressMessages(library(IRanges))
 > myranges <- IRanges(start = c(1,3,5,7), end = c(2,4,8,9))
 > names(myranges) <- c("a", "b", "c", "d")
 > myranges
IRanges object:
  start end width names
1     1   2     2     a
2     3   4     2     b
3     5   8     4     c
4     7   9     3     d
 > myranges[c("c", "a", "d", "b")]
IRanges object:
  start end width names
1     5   8     4     c
2     1   2     2     a
3     7   9     3     d
4     3   4     2     b
 > sessionInfo()
R version 2.9.0 Under development (unstable) (2009-01-19 r47650)
i386-apple-darwin9.6.0

locale:
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_1.1.34

loaded via a namespace (and not attached):
[1] grid_2.9.0         lattice_0.17-20    Matrix_0.999375-18



Daniel Brewer wrote:
> Hello,
>
> Is there any way to add rownames to an IRanges object?  What I am trying
> to do is try and make it easy to reference back to the original table
> that created the IRanges object after an overlap.
>
> Hs1plus <- with(HsapiensAnnot[HsapiensAnnot$seqname == "1" &
> HsapiensAnnot$strand == "+",], IRanges(start, end))
>
> yoda1plus <- with(yip[yip$seqname == "chr1" & yip$strand == "+",],
> IRanges(start, end))
> yoda1plus <- yoda1plus[order(start(yoda1plus)),]
>
> seqoverlap <- overlap(Hs1plus,yoda1plus,multiple=F)
>
> At the moment to get information about the overlaps I have to do
> something like:
> HsapiensAnnot[HsapiensAnnot$start == start(Hs1plus[seqoverlap[1],]) &
> HsapiensAnnot$seqname=="1",]
>
> but I am sure that there is a better way and this can't deal with the
> NAs that might be in seqoverlap
>
> Thanks
>
> Dan
>