[Bioc-sig-seq] Consolidate AlignedRead objects

[Martin Morgan]

Hi Ivan --

Ivan Gregoretti wrote:
> Hello everybody,
> 
> Is there any memory efficient way to consolidate multiple AlignedRead
> objects into one?
> 
> 
> Example:
> 
> Lets say that I have 10 AlignedRead instances, 10 million tags each.
> Lets call those instances aln01 through aln10.
> 
> I can consolidate two of them like this:
> 
> aln <- append(aln01, aln02)

I don't think there's anything built-in. You could try this

   superDuperConsolidator <- function(...)
      Reduce(append, list(...))

it might not be too bad memory-wise.

Martin

> 
> Can I consolidate all AlignRead instances in a single shot? Something like this:
> 
> aln <- superDuperConsolidator(aln01, aln02, aln03, ..., aln10)
> 
> Thank you,
> 
> Ivan
> 
> #########################################################
>> sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-08-12 r49169)
> 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] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] ShortRead_1.3.27   lattice_0.17-25    BSgenome_1.13.10   Biostrings_2.13.34
> [5] IRanges_1.3.60
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.5.5 grid_2.10.0   hwriter_1.1
> 
> #########################################################
> 
> Ivan Gregoretti, PhD
> National Institute of Diabetes and Digestive and Kidney Diseases
> National Institutes of Health
> 5 Memorial Dr, Building 5, Room 205.
> Bethesda, MD 20892. USA.
> Phone: 1-301-496-1592
> Fax: 1-301-496-9878
> 
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793