Step 4. Prepare the covariates file for TensorQTL mapping - ariadnacilleros/Cis-mQTL-mapping-protocol-for-methylome GitHub Wiki

In this analysis, the covariates that we are going to use are the sex of the samples, the planet values obtained through preprocessingofData() function in Step 2.1., and the Principal Components of our genotype. The number of PCs to use as covariates will be defined by your data, in this analysis, we have used the first five PCs as an example. Therefore, we will need to perform a Principal Component Analysis (PCA) of the final genotype set that we obtained in Step 3. Once we have the Principal Components computed by PLINK, you can use the commands in the RScript proposed in the Readme, to create the text file of the covariates for TensorQTL, but you will need to specify the file from which you obtain the sex of the samples. You can see an example of the final text file on the Readme.