Last modified: 1st November 2017 Instructions to obtain a Principal Component Analysis from public datasets We need a parameter file for smartpca. For example I used the file smartpcaMinSS.par: genotypename: MinSS.geno snpname: MinSS.snp indivname: MinSS.ind evecoutname: MinSS.pca.evec evaloutname: MinSS.pca.eval numoutevec: 10 numoutlieriter: 0 maxpops: 100 poplistname: poplistname.txt snpweightoutname: MinSS.snpweight lsqproject: YES The first three lines … Continue reading Principal Component Analysis (PCA) with Eigensoft and R