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
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