[BioC] Cannot call ShortRead package FastqSampler from Linux

[Martin Morgan]

Hi Tal --

On 05/30/2012 01:35 PM, talshay wrote:
> Hi,
>
> I have huge Fastq paired RNA-seq file that I am trying to down-sample.
> It seems ShortRead Package 1.6.2 FastqSampler class should do that, but
> I can't call it from Linux.

FastqSampler was not available in R-2.11 / ShortRead 1.6.2; likely your 
Windows system has a newer version of both R and ShortRead.

I strongly recommend updating to the current R -- R-2.15 -- and hence 
ShortRead (1.14.4).

Martin

>
>  > library("ShortRead")
>  > f1 <- FastqSampler(file_name, n=50)
> Error: could not find function "FastqSampler"
>  > getClassDef("FastqSampler")
> NULL
>
> Session info below shows that the package is loaded - what am I missing
> here?
> FastqSampler is documented as a class and not a method, but all samples
> I found seem to be using it the same way, and it is recognized when I do
> the same on my Windows PC.
>
> Thanks for any help,
> Tal
>
>  > sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] ShortRead_1.6.2 Rsamtools_1.0.1 lattice_0.18-5
> [4] Biostrings_2.16.9 GenomicRanges_1.0.9 IRanges_1.6.17
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2
>
>
> This seems to be specific to the Linux version, as when I do the same on
> my Windows PC, FastqSampler is recognized.
>
>  > getClassDef("FastqSampler")
> Reference Class "FastqSampler":
>
> Class fields:
>
> Name: con reader readerBlockSize recParser recSeperator n saved_n tot_n
> records buf verbose
> Class: ANY function integer function raw integer integer integer list
> raw logical
>
> Class Methods:
> ".add", ".flush", ".getCurrent", ".sampler_msg", "callSuper", "export",
> "get", "import", "initFields", "reset", "sample", "status"
>
>
> Reference Superclasses:
> "Sampler", "envRefClass"
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor


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

Location: M1-B861
Telephone: 206 667-2793