Circumvent creating .ff files in the working directory when using genotype.Illumina() function
1
0
Entering edit mode
komal.rathi ▴ 80
@komalrathi-9163
Last seen 4 weeks ago
United States

Hi,

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(),  : 

  write error

Is there an option where you can circumvent the creation of these files?

Thanks!

crlmm genotype.Illumina ff • 661 views
ADD COMMENT
0
Entering edit mode
Katsura • 0
@katsura-15097
Last seen 3.6 years ago
China

Are you solving the problem now? I encountered the same problem  :)

ADD COMMENT

Login before adding your answer.

Traffic: 335 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6