Question: Regression error using GENESIS to perform GWAS
gravatar for jjackson
2.2 years ago by
jjackson0 wrote:

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
[1] 0.0100000 -6068.9203405 0.9978943
[1] 9.999474e-03 -6.068920e+03 9.978944e-01
[1] 4.508873e-03 -6.068887e+03 9.992358e-01
[1] 4.461980e-04 -6.068867e+03 1.000238e+00
[1] 6.909751e-05 -6.068865e+03 1.000331e+00
[1] 2.346956e-05 -6.068865e+03 1.000342e+00
[1] 0.000000 -6068.864949 1.000348
Error in solve.default(AI, score) : 'a' is 0-diml

Does anyone have any idea what this means?

genesis • 802 views
ADD COMMENTlink modified 13 months ago by jjw170 • written 2.2 years ago by jjackson0
gravatar for jjw17
13 months ago by
jjw170 wrote:

Did you ever figure out this issue? I am having the same error with fitNullMM() in GENESIS. I've spent all day trying to figure it out.

ADD COMMENTlink written 13 months ago by jjw170

It seems to work with fitNullMM(scanData, family= binomial, dropZeros =F) or with family = gaussian rather than binary

ADD REPLYlink written 13 months ago by jjw170
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