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"

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