vtools associate qualtitative phenotypes

[fabiennejh]

Hello,

is it possible to use a qualitative phenotype in variant tools (with my own R test) ? I tried, but received the following error message :

Invalid (non-numeric) coding in phenotype/covariates values

Thank you for your answer ! best Fabienne

[gaow]

@fabiennejh it would be very helpful if you could provide a minimal working example to us, including a very small vtools project, your customized R test script and the command you used. Possibly start from the command you used? If it is your own R test we should not check if a test only works for case/ctrl data and throw that error ..

[fabiennejh]

Here is the command line I used. vtools associate RYR3_lowEXAC_SNP groupe_T4 --samples "groupe_T4 is not NULL" --discard_variants "%(NA) >0.40" -m "RTest CAST_order.R --phenotype.name 'groupe_T4' --MAF.filter 0.2 --MAF.grp 'all' --class.order 'MILD,MODERATE,SEVERE'" --group_by Gene_name --jobs 8

I tried to give you a copy of my vtools project, with essential data. I don't give you the Rscript, but it shoudn't be a problem because the error comes before running the R script if I understand correctly.

Best Fabienne

[gaow]

@fabiennejh I cannot unzip the file you uploaded. Could you verify you can download it, unzip and be able to run vtools command on it?

[fabiennejh]

It's not a real zip file. I added the .zip extension to be able to upload the file in Github. You only need to delete the extension.

[gaow]

We need the genotype database as well -- *.proj will not work.

[fabiennejh]

It's too big to load it here ....

[fabiennejh]

Here are the .proj and DB files RYR3_genotype.DB.gz RYR3.proj.gz

[fabiennejh]

Hello Did you solve the problem ? Best Fabienne