Missing genotype compatible

[sinarueeger]

Hi @diptavo,

I have noticed that missing genotype data results in an error in a basic MultiSKAT model.

library(MultiSKAT)
#> Loading required package: SKAT
#> Loading required package: nlme
#> Warning: package 'nlme' was built under R version 3.5.2
#> Loading required package: copula
#> Warning: package 'copula' was built under R version 3.5.2
data(MultiSKAT.example.data)
attach(MultiSKAT.example.data)

## Introduce NAs in Genotypes
Genotypes[1,1] <- NA

obj_null <- MultiSKAT_NULL(Phenotypes, Cov)

MultiSKAT(obj_null, Genotypes, Sigma_p = cov(Phenotypes), verbose = FALSE)
#> Error in if (mf[i] > 0.5) mf[i] = 1 - mf[i]: missing value where TRUE/FALSE needed

detach(MultiSKAT.example.data)

^{Created on 2019-06-11 by the reprex package (v0.2.1)}

Bug fix

I found that the error message stems from theMAF function stored in R/helpers.R. More specifically, MAF contains a sum function that will yield in NA, if the G matrix contains any NAs.
I have added an na.rm = TRUE to the sum function.

I have also added a unit test that will fail with the version you currently have on the master, but pass with my version.

I let you choose what kind of files you want to merge into your master.