Hi, I am trying to correlate allele frequencies for two populations. My datasets are binary (bed, bim, fam), exported from Plink and read into R using read.plink (snpStats). I want to generate a correlation matrix for the two populations and thought I would use cor.test (method = ?spearman?) to do this. R is interpreting my genotype data as a matrix; I have 45 individuals and 100 000 loci in each dataset. I tried coercing each to numeric with as.data.frame(x), but this method is just hanging. I don?t know whether the size of the dataset is the problem or if it?s the structure of the data. Please assist. Regards, Ceci Sent from Mail for Windows 10 [[alternative HTML version deleted]]