I am using the `genotype.Illumina` function from `clrmm` package. This is my code:
library(crlmm) library(ff) cnSet <- genotype.Illumina(sampleSheet=samplesheet, arrayNames=arrayNames, arrayInfoColNames=arrayInfo, cdfName="human610quadv1b", batch=batch)
Now when running this function, a lot of .ff files are created in the working directory and it is causing a problem because after a point when the number of files are large, I get an error:
Instantiate CNSet container.path arg not set. Assuming files are in local directory, or that complete path is provided
Initializing container for genotyping and copy number estimation
Error in ff(initdata = initdata, vmode = vmode, dim = dim, pattern = file.path(ldPath(), :
Is there an option where you can circumvent the creation of these files?