Arguments eqtl.lis and snp.dat

[gprashant17]

How exactly do we obtain the arguments eqtl.lis and snp.dat for the function MixRF.impute from publicly available GTEx data (RNA-seq)? The documentation says that we have to obtain the snp.dat argument, after which we can generate the eqtl.lis argument by making use of the code in eqtl.r. So in order to obtain genotype matrix, do we have to make use of the eqtl data available for each tissue in the GTEx portal?

[randel]

First of all, you should have access to the protected genotype data. It requires application via dbGaP. The GTEx portal only stores public data, e.g., eQTL lists and RNA-seq data. https://gtexportal.org/home/protectedDataAccess

Then you can either use public eQTL list or calculate eQTLs using our function. eqtl.lis denotes the eQTL list (e.g., SNP name for each gene), and snp.dat represents the genotype data.

[gprashant17]

Thanks for the information. I will have a look into it.

Moreover, I am assuming that the genotype data conveys whether an individual has a particular mutation (SNP) or not. I looked at the SNP data of the simulated dataset, which was filled with 0s, 1s and 2s as well. What do those 2s represent? Or am I assuming something incorrectly?

[randel]

Usually, an SNP consists of two alleles (say A or a). AA, Aa, and aa can be coded as 0, 1, and 2 based on the number of allele a.