[R] Help with Allele frequency correlation

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

[R] Uni and multivariate analyses on binary data

Hi, I have a large data set in binary code, no covariates. Say, positions along a genomic sequence where reference sequence is represented by 0 and changes represented by 1. I have 99 positions and 2000 sequences to analyze. I want to run a univariate analysis to isolate positions where majorit