I'm struggling these last days on a case/control phenotype prediction problem based on genotype (individual x SNPs with more than 10k individuals and approx 18k SNPs encoded as 0,1,2).
Thanks to PCA analysis (with SNPRelate package), I observed that there are sub-populations in my training set. I suspect that there is a bias in my classifier due these sub-population.
My current methodology to improve my classifier accuracy is the following:
- build one model for each population,
- during prediction phase based on test dataset -> assign each individual to one of the population identified previously. Apply the model built for this population.
- which packages and methods in R would you advise me to assign a cluster to each of my individual ? Could I use PC eigenvectors to achieve such clustering ?
- which packages and methods in R could allow me to associate training genotype to cluster prior to apply the specific model ?
Thank in advance for your help.