[BioC] Biostrings - size limits
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Thu Jun 24 17:57:59 CEST 2010
On Thu, Jun 24, 2010 at 9:24 AM, Erik Wright <eswright at wisc.edu> wrote:
> What limits the number of sequences and size of sequences that are part of a DNAStringSet?
(1) the amount of RAM on your computer, and;
(2) the architecture (32 bit vs. 64 bit) that R is running on/in.
> Are there any way to change these limits?
Yes, adjust (1) and (2) from above.
> On my home laptop I can create a DNAStringSet of about sixty thousand sequences of length 1500. On my desktop I can only make a DNAStringSet of twenty thousand sequences.
What's the error you get when you try to create these large
DNAStringSets on your desktop?
> Does anyone know what is creating this difference is maximum size?
What are the differences between the computers, specifically with
respect to RAM and architecture?
> Is there any way I can "up" the amount of memory available to a sequence set? I would like to be able to have at least one hundred thousand sequences (of width 1500 nucleotides) in memory.
R wouldn't limit the amount of memory on a per object basis[*] -- it
just takes as much RAM as it can get from the OS.
[*] with the exception of the number of elements in a vector, which is
limited to 2^(32-1) due to R's 32bit addressing for vectors, but AFAIK
(i) Biostrings runs an end-around on this to avoid this problem, and
(ii) you're only talking about 100,000 elements anyway, so this isn't
>R version 2.11.0 (2010-04-22)
Is this for your laptop, desktop, or both?
Also, R 2.11.1 is out -- never hurts to upgrade ;-)
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
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