I apologize if this is incredibly asinine, but how can I view my ped file as a matrix in R? I've been using plink to do some analyses on a bunch of chip-seq data we have, but we want to separate the cases from the two studies that make up our dataset. I plan on utilizing some sort of "if, else" function for the actual sorting, but I need to be able to view the Individual IDs in order to write that line of code.
1- What package should I install to do this?
2- What function lets me view my file in a matrix?
I'm running R version 3.3.1 and some of the more popular package options according to Google don't seem to work with my version (SNPRelate, SNPStats). I have downloaded genetics and GenAbel but I don't seem to be able to pull my file up in the way I wish to view it.
Thanks in advance!