Assessing conditional independence of genes in Trans-eQTL cluster I've identified a Single Nucleotide Polymorphism (SNP) that is associated with a variable of interest (lets just call it height) using a Genome Wide Association Study (GWAS). The SNP can be of the values A/A, A/G or G/G in each of the 69 samples.
I also have gene expression data for the 69 samples and it appears that the SNP is affecting the expression of a large number (~500) genes. I'm wondering if there is a convenient statistical package/technique available to assess if the variable (height) becomes independent of genotype (A/A, A/G or G/G) conditioning on the expression of each of the ~500 genes who's expression are associated with the SNP (i.e. assessing conditional independence of each of the ~500 genes)?
 A: I would recommend looking at the snpMatrix R package. Within the snp.lhs.tests() function, height will be the phenotype (or outcome), your SNP data will be stored in a vector (snp.data), and your gene expression levels will enter the model as covariates. I never used this kind of covariates (in the GWAS I am familiar with we adjust for population stratification and subject-specific covariates), so I can't give an example of use. Just give it a try to see if it suits your needs.
Otherwise, a larger modeling framework is available in the GGtools package, from the Bioconductor project too.  It was developed by Vince J. Carey for dealing specifically with SNP and gene expression data, in GWAS or eQTL studies. There are numerous examples of use on the web (look up for tutorial by VJ Carey with GGtools). However, it's mainly to model gene expression as a function of observed genotypes (chromosome- or genome-wide).
Caution. Please note that GGtools package has a lot of dependencies, in particular GGBase (which provides specific environments for holding genetic data) and snpMatrix (which an provides an efficient storage of SNP data). You will also need to install the base packages from the Bioconductor repository (this is not part of CRAN); detailed instructions are available here.
