copy number variation as a covariate in MatrixEQTL

Question

[mms140130]

I want to add the copy number variation as a covariate in the model by MatrixEQTL, but I have 20,000 rows and 1069 columns, this won't work as the number rows is greater than the number of samples

How can I fix that?

Answer 1

[Fabio Marroni]

I don't think that adding 20,000 covariates is a good idea. You should do a PCA analysis on the CNV data and then use the first X components (where X is a number between 2 and 10, let's say) as covariates. PCA can used to correct for population structure (doing PCA on the genotype data) or to incorporate unaccounted bias in genotypes (e.g. I also suggest that you use as a covariate the PCA of your expression data). There is lot of discussion on the use of PCA in GWAS. You will find useful references here.