I'm in the process of performing a genetic association test on WGS data using Bioconductor packages and I'm at a road block. My workflow (simplified) looks like this:
1) (convertVCF2GDS.R) Convert my VCF files to GDS files using SNPRelate
2) (relatednessMatrix.R) Using the SNPRelate package, I filter the SNPs in my GDS file via LD Pruning (snpgdsLDPruning) and compute a GRM matrix (snpgdsGRM). I then export the matrix to a csv.
3) (GENESIS-1.0.R) I import the genotype/phenotype files, matrix csv and the vector of pruned SNPs and fit the null model with a binomial error distribution using as input:
a) a scanAnnotationDataFrame object created from the phenotype file
b) a vector of sample ids to include
c) the imported matrix
When I run the following line of code:
nullmod.SNPRelate <- fitNullMM(scanData = SNPRelate.scanAnnot, outcome = "pheno", family = binomial, covMatList = cgtaMatrix, verbose=TRUE, scan.include=both)
it runs for a moment and then gives an error:
Reading in Phenotype and Covariate Data... Fitting Model with 2872 Samples Computing Variance Component Estimates using AIREML Procedure... Sigma2_A log-lik RSS  0.0100000 -6068.9203405 0.9978943  9.999474e-03 -6.068920e+03 9.978944e-01  4.508873e-03 -6.068887e+03 9.992358e-01  4.461980e-04 -6.068867e+03 1.000238e+00  6.909751e-05 -6.068865e+03 1.000331e+00  2.346956e-05 -6.068865e+03 1.000342e+00  0.000000 -6068.864949 1.000348 Error in solve.default(AI, score) : 'a' is 0-diml
Does anyone have any idea what this means?