[BioC] GRanges, strange behavior when chromosomes don't match

[Cei Abreu-Goodger]

Hello all,

When you have two GRanges objects which don't have the same seqnames 
factor, you can get very unexpected behavior.

Would it be possible to get an error/warning when this is attempted? I 
don't know how many functions are affected, perhaps the functions 
mentioned below can be modified to produce a more obvious result...

Many thanks,

Cei


Code example / sessionInfo:

library(GenomicRanges)
gr1 <- GRanges(seqnames = c("chr1", "chr2", "chr3", "chr4"),
           ranges = IRanges(1:4, width = 10),
           strand = c("-", "+", "+", "+"))
gr2 <- GRanges(seqnames = c("chr1", "chr2", "chr5", "chr6"),
           ranges = IRanges(1:4, width = 10),
           strand = c("-", "+", "+", "+"))

union(gr1,gr2)
# gives expected result, all 6 ranges

intersect(gr1,gr2)
# includes ranges from the missing gr2 chromosomes

setdiff(gr1,gr2)
# includes 3 copies of the ranges from the missing gr2 chromosomes


sessionInfo()
R version 2.11.0 (2010-04-22)
i386-apple-darwin9.8.0

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] GenomicRanges_1.0.5 IRanges_1.6.8       Biobase_2.8.0

loaded via a namespace (and not attached):
[1] tools_2.11.0