Set.Threshold M.eff

[ryan-earp]

I am trying to follow the vignette using the set.threshold command and get the following error:
set.threshold(data.original.scan,method="M.eff",level=0.05)
Error in cor(data@geno[, ix]) :
supply both 'x' and 'y' or a matrix-like 'x'

The genotype file was created using the VCF2dosage command from a VCF created using Freebayes.
Have you seen this before or know how to correct this issue?
Thanks!

[jendelman]

I am not sure what is causing this error. Did you inspect the CSV output from VCF2dosage? Does every chromosome have at least 1 marker?

[ryan-earp]

Just checked and there is not at least one marker per chromosome. There is also a good bit of missing data as a result of the VCF2dosage that was imputed with the population mode which I saw was not recommended.