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smgogarten / GWASTools

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis
https://bioconductor.org/packages/GWASTools
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GdsGenotypeReader error #12

Closed EDISON2022W closed 1 year ago

EDISON2022W commented 1 year ago

I used the command

GWASTools::gdsSubset(input, sub.input, sample.include=IDuse, snp.include=snpuse) to subset the gds file.

Then I checked the file using

GWASTools::gdsSubsetCheck(input, sub.input, sample.include=IDuse, snp.include=snpuse)

It returned "All variables match."

Finally, I used the command

GdsGenotypeReader("sub.input") to read the file.

It returned an error

Error in validObject(.Object) : invalid class “GdsGenotypeReader” object: genotype order is not specified: 'snp,scan' or 'scan,snp'

I would appreciate it if you could help me with the problem. Thanks!