I think you are fundamentally confused about why you would use PICs in the first place.

Joe Felsenstein showed that data points from organisms are not independent due to their shared ancestry. You calculate PICs in order to make your data points IID. The theory behind this is beyond the scope of this post.

One assumption of PICs is that the traits evolve by Brownian motion, a simplistic process with nice mathematical properties. Your inputs, at least in the ape R package, are the tree relating your individuals and a list of the phenotypic traits (i.e., body size, brain size, etc.). These trait values are then 'corrected' using the phylogeny, and it is then possible to make statistical inferences from them.

TL; DR: you want to give pic() a vector of trait values, not the loci underpinning them.