plink2R natively reads PLINK (http://pngu.mgh.harvard.edu/~purcell/plink) BED/BIM/FAM files into R.
Missing genotypes are imputed by assigning missing values the per-SNP average.
Depends on Rcpp, RcppEigen
Example:
library(plink2R)
dat <- read_plink("data")
dim(dat$bed)
dim(dat$fam)
dim(dat$bim)
Also see the file plink2.R for an example.
If there are missing genotypes, these will by default be assigned as NA. To do
simple imputation of missing genotypes (for each SNP, randomly assigning to
the missing genotypes values sampled proportionally to the non-missing
genotypes in the SNP), use read_plink("data", impute="random").