[BioC] Merging RandData object with names on the IRanges part

[Ulrike Goebel]

Dear list,

I would like to do the following:
Read an output file of BWA (SAM format) in "chunks"  and incrementally 
build a RangedData object from
the chunks (by 'rbind') . Ultimately that should be used to get the 
number of reads per annotated transcript/region, but this is not the 
question here.

Assume as an example:
t1 <- RangedData(IRanges(start=c(7828367, 7828552,4121953), 
end=c(7828402, 7828587, 4121988)), space=c("Chr1", "Chr1", "Chr3"), 
mapq=c(1,2,1),flag=c(3,4,5))

I can merge two copies of this by 'rbind(t1,t1)'.

But:
t2 <- RangedData(IRanges(start=c(7828367, 7828552,4121953), 
end=c(7828402, 7828587, 4121988), names=c("a", "b", "c")), 
space=c("Chr1", "Chr1", "Chr3"), mapq=c(1,2,1),flag=c(3,4,5))
(Here, I would like to keep the read names along with their positions in 
the IRanges object).

 > rbind(t2,t2)
Error in validObject(.Object) :
  invalid class "RangedData" object: the names of the ranges must equal 
the rownames

Am I doing something completely wrong here ? Or is it confusing two 
different meanings of 'names' ?


BTW, I really like IRanges !

Ulrike
 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-08-01 r49053)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] ChIPR_1.1.3          MASS_7.3-0           spatstat_1.16-1
 [4] deldir_0.0-8         gpclib_1.4-4         mgcv_1.5-5
 [7] convert_1.21.1       marray_1.23.0        matchprobes_1.17.0
[10] AnnotationDbi_1.7.11 Biostrings_2.13.29   TeachingDemos_2.4
[13] Ringo_1.9.8          Matrix_0.999375-30   lattice_0.17-25
[16] limma_2.19.2         RColorBrewer_1.0-2   Biobase_2.5.5
[19] IRanges_1.3.56

loaded via a namespace (and not attached):
 [1] affy_1.23.4          affyio_1.13.3        annotate_1.23.1
 [4] DBI_0.2-4            genefilter_1.25.7    nlme_3.1-92
 [7] preprocessCore_1.7.4 RSQLite_0.7-1        splines_2.10.0
[10] survival_2.35-4      tools_2.10.0         xtable_1.5-5




-- 
  Dr. Ulrike Goebel
  Bioinformatics Support
  Max-Planck Institute for Plant Breeding Research
  Carl-von-Linne Weg 10
  50829 Cologne
  Germany
  +49(0) 221 5062 121