SKAT error when including covariates

[mimi_lupton]

I am using the SKAT program in R to try and analyse a small subset of data for just one gene looking at certain rare variants.
I run into an error when I try and add covariates into the model.
I would really appreciate any help at all, or a hint of what could be wrong!

I am doing the following;

Use Generate_SSD_SetID to create SSD and Info files from the plink files.

Use Read_Plink_FAM_Cov to read in the Fam and cov files, I have three covariates, and the file looks like this;

> FAM_Cov[1:5,]
FID IID PID MID Sex Phenotype COV1 COV2 COV3
1 GKAD0335 GKAD0335 0 0 1 1 1 0 89
2 GKAD0874 GKAD0874 0 0 2 1 2 1 80
3 GKAD0364 GKAD0364 0 0 1 1 1 1 86
4 GKAD0412 GKAD0412 0 0 2 1 2 0 NA
5 GKAD0393 GKAD0393 0 0 2 1 2 0 85

then I do;

> y<-FAM_Cov$Phenotype
> X1 = FAM_Cov$COV1
> X2 = FAM_Cov$COV2
> X3 = FAM_Cov$COV3

> SSD.INFO<-Open_SSD(File.SSD, File.Info)
> obj<-SKAT_Null_Model(y ~ X1 + X2 + X3, out_type="D")
> SKAT.SSD.All(SSD.INFO, obj)

$results
SetID P.value N.Marker.All N.Marker.Test
1 gene NA NA NA

$P.value.Resampling
NULL

attr(,"class")
[1] "SKAT_SSD_ALL"
Warning message:
Error to run SKAT for gene: Error in as.matrix(Z[id_include, ]) : subscript out of bounds