The snps package contains helper functions for manipulating marker
genotypes stored in a numeric matrix. Functions are provided for
calculating minor allele frequency, filtering SNPs, pruning SNPs in high
linkage disequilibrium, etc.
This package is not very complete, thorough, or extensive. It is simply a code organization tool.
You can install the package using devtools::install_github():
if (!require(devtools)) install.packages("devtools")
devtools::install_github("neyhartj/snps")