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

[Michael Dondrup]

Hi Ulrike,

I think you can use function c().
you then can get the IRanges names preserved in your examples:

 > ranges(c(t1,t2))[[3]]
IRanges object:
      start     end width names
[1] 7828367 7828402    36     a
[2] 7828552 7828587    36     b


Michael

Am 20.08.2009 um 17:03 schrieb 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
>
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Michael Dondrup, Ph.D.
Bergen Center for Computational Science
Computational Biology Unit
Unifob AS - Thormøhlensgate 55, N-5008 Bergen, Norway
Phone: +47 55584029 Fax: +47 55584295