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  • SKAT error when including covariates

    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
    Last edited by mimi_lupton; 07-30-2013, 03:42 PM.

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