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 !