Question about GWASTools gdsSubset
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SuperD • 0
@65c75c16
Last seen 14 months ago
United States

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 anyone could help me with the problem. Thanks!

GWASTools gdsSubset • 819 views
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@stephanie-m-gogarten-5121
Last seen 21 days ago
University of Washington

GdsGenotypeReader will attempt to determine the dimensions of your file automatically, but if it can't (e.g. if the number of snps and scans is the same), it will issue that error and require you provide the argument genotypeDim='snp,scan' or 'scan,snp'.

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Is there any way to infer 'snp,scan' or 'scan,snp' format for a gds file?

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You could see if an attribute has been set on the genotype node indicating the order:

> library(gdsfmt)
> gdsfile <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
> gds <- openfn.gds(gdsfile)
> get.attr.gdsn(index.gdsn(gds, "genotype"))
$snp.order
NULL

Seeing snp.order here means the dimensions are snp,scan, while sample.order would indicate scan,snp.

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