GWAS: attempt to set 'colnames' on an object with less than two dimensions about bgdata HOT 5 CLOSED

Thanks for the detailed report. Could you please confirm that the alternate phenotype file has been correctly loaded, i.e., if bg@pheno contains the my_phenodata column with valid data?

from bgdata.

It appears to me that it has been loaded correctly.

> bg@pheno
                 FID     IID my_phenotype
201782_400194 201782  400194   NA
201782_400495 201782  400495    0

Here's the tab-separated file I loaded in:

>head -n 3 REP_2_SW3_TDZ_withheader
FID	IID	my_phenotype
201782	400194	NA
201782	400495	0

from bgdata.

What version of BGData are you using? You can check with packageVersion("BGData").

from bgdata.

I'm on version 2.0.0. Please let me know if anything else would be helpful to figure this out.

> packageVersion("BGData")
[1] ‘2.0.0’

from bgdata.

Sorry, I forgot to follow up on this issue... If you are still interested, could you please run your GWAS call again with nCores = 1, i.e. gwas <- GWAS(formula = my_phenotype ~ 1, data = bg, nCores = 1)? This should give you a better error message. The package we use for multi-core computations swallows error messages unless explicitly handled, which I have just addressed in 47e89bb (an alternative would be to try running the code again with the development version).

from bgdata.