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
[email protected]
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
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
