[BioC] Cannot call ShortRead package FastqSampler from Linux
talshay
talshay at broadinstitute.org
Wed May 30 22:35:44 CEST 2012
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.
> 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"
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