I am mapping the SNP to gene expression to find the cis and trans eQTL.
First I tried the R package MatrixEQTL, however, finding too much trans-eQTLs, which make me doubt about the results. Even I appied several covariates to adjust the results, it seems the condition is not changed.
So here is the problem, which approach should I use to do the mapping, since r/qtl seems little complex to me and plink requires too much time for calculation.
Now i have the genotyping data with plink bed format, and an expression matrix for ~20k genes.
Could some one help me, and some step-by-step tutorials?