I have performed logistic regression on 3 independent sets of case/control cohorts. I now have the task of figuring out how well a collection of the SNPs implicated in the study predict disease/control status of the individual.
The package I am trying to use in R is ROCR however I cannot figure out how I should generate the prediction object and other files needed to start the process. The code looks very simple and straight forward but I am struggling with getting started.
Any idea how I can generate the prediction object and other files for several hundred SNPs ? I have the statistical values generated from the logistic regression analysis for all the SNPs as well as the affliction status of the 3 cohorts.
I appreciate any help you can provide.