Thank you! That helped me a lot.
A further question: Is there any way to access the complete DNAStringSet
"dnaS" after I removed it using the rm() function? If not, keeping the
complete DNAStringSet in memory does not make much sense to me.
Thank you,
Hans-Ulrich
Vincent Carey wrote:
see the information on compact() method in XStringSet-class
package:Biostrings R Documentation
to rationalize this you need to think about the difference between a
view and a concrete instance. typically you do not want a copy to be
made on each view
On Thu, May 27, 2010 at 10:21 AM, Hans-Ulrich Klein
<[email protected] <mailto:[email protected]>> wrote:
Hi all,
I observed that some DNAStrings (and also DNAStringSets) objects
are to large after subsetting:
> library("Rsamtools")
> parameters = ScanBamParam()
> bam = scanBam("data/N01.bam", param=parameters)
> ss = bam[[1]]$seq
> ss
A DNAStringSet instance of length 230980
[...]
> print(object.size(ss), units="Mb")
83.3 Mb
> dnaS = ss[[5]]
> dnaS
128-letter "DNAString" instance
seq:
TAGCGTGGATACAGAGGGACATCTATTGACCAGCTA...AAAGTTGTGCTTTATTTGATGAATAAGTATTGAACA
> print(object.size(dnaS), units="Mb")
80.7 Mb
> print(object.size(as.character(dnaS)), units="Kb")
0.2 Kb
When I write the 128-letter DNAString to disk, it remains quite
large (~ 20Mb).
Best wishes,
Hans-Ulrich
> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-pc-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rsamtools_1.0.1 Biostrings_2.16.2 GenomicRanges_1.0.1
[4] IRanges_1.6.4
loaded via a namespace (and not attached):
[1] Biobase_2.8.0
--
Hans-Ulrich Klein
Department of Medical Informatics and Biomathematics
University of Münster
Domagkstrasse 9
48149 Münster, Germany
Tel.: +49 (0)251 83-58405
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--
Hans-Ulrich Klein
Department of Medical Informatics and Biomathematics
University of Münster
Domagkstrasse 9
48149 Münster, Germany
Tel.: +49 (0)251 83-58405
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
