Simple imputation based on allele frequencies

This function provides a very simple imputation algorithm for gen_tibble objects by using the mode, mean or sampling from the allele frequencies. Each locus is imputed independently (and thus linkage information is ignored).

Usage

gt_impute_simple(x, method = c("mode", "mean0", "random"), n_cores = 1)

Arguments

x

a gen_tibble with missing data

method

one of

• 'mode': the most frequent genotype

• 'mean0': the mean rounded to the nearest integer

• 'random': randomly sample a genotype based on the observed allele frequencies

n_cores

the number of cores to be used

Value

a gen_tibble with imputed genotypes

Details

This function is a wrapper around bigsnpr::snp_fastImputeSimple().