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Question: QuasR - preprocessReads fails with a SRFilterResult error
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gravatar for jlncrnt
9 weeks ago by
jlncrnt10
jlncrnt10 wrote:

Hi,

I'm facing an issue when calling the preprocessReads() function in the QuasR package. I adapted the example in the doc to my needs. The code is very similar :

td <- tempdir()
infiles <- file.path("myfile.fastq.gz")
outfiles <- file.path(td, basename(infiles))
res <- preprocessReads(filename=infiles, outputFilename=outfiles,truncateEndBases=1, Rpattern="CTGTAGGCACCATCAATAGATCGGAA",minLength=20,nBases=1)
unlink(outfiles)

QuasR ouputs the following error :

Error in value[[3L]](cond): Filter 'CleanNFilter' failed: invalid class "SRFilterResult" object: superclass "Mnumeric" not defined in the environment of the object's class

...followed by the stack trace. I'm struggling with it for quite a bit of time now and I'm using cutadapt to keep moving, but it would be nicer if I could stay in the same ecosystem for reads preprocessing and analysis. What am I doing wrong ? I didn't found any help on docs, but maybe I haven't looked enough...

Here is my sessionInfo() :

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Thank you !

 

edit:

packageVersion("QuasR")
'1.14.0'
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by jlncrnt10
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