[R] Help with Allele frequency correlation

Busisiwe Mlotshwa cb.mlotshwa at gmail.com
Fri Feb 19 04:27:51 CET 2016

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.


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