Hi all,
I have just started learning GWAS as I will have to run some of them in the near future and I am pretty confused about which are the best computational tools available for my dataset. In particular, I have almost 10 millions SNPs that I would like to test against clinical numerical covariates such as blood pressure. Moreover, I have some high-dimensional phenotypes that I would like to reduce to 40/50 variables using PCA or ICA and test them in the same multivariate model.
I have been advised to use the R package matrix EQTL for univariate (linear regression) models and from their paper the GEMMA software (http://www.xzlab.org/software.html) looks promising for multivariate ones. However, I would like to year your thoughts about this before starting, please.
Many thanks!
I am not an expert on GWAS but if you want to do this in R I would take a look at Bioconductor. In particular the packages related to GWAS. Also search for QTL or other terms of interest in the view of available packages.
PLINK currently only supports univariate models, and it is not optimized for a huge number of phenotypes in the way Matrix eQTL is.
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