Question

Question about GWASTools gdsSubset

0

Entering edit mode

SuperD • 0

@65c75c16

Last seen 22 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 • 1.2k views

ADD COMMENT • link written 22 months ago by SuperD • 0

score 1 · Answer 1 · 2023-02-06

1

Entering edit mode

Stephanie M. Gogarten ▴ 870

@stephanie-m-gogarten-5121

Last seen 5 months 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'.

ADD COMMENT • link 22 months ago Stephanie M. Gogarten ▴ 870

0

Entering edit mode

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

ADD REPLY • link 22 months ago SuperD • 0

1

Entering edit mode

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.

ADD REPLY • link 22 months ago Stephanie M. Gogarten ▴ 870