gt_impute_simple: Simple imputation based on allele frequencies

In tidypopgen: Tidy Population Genetics

Simple imputation based on allele frequencies

Description

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

Details

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

Value

a gen_tibble with imputed genotypes

Examples

example_gt <- load_example_gt("gen_tbl")

# Impute the gen_tibble
example_gt <- example_gt %>% gt_impute_simple()

# And we can check it has been imputed
example_gt %>% gt_has_imputed()

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.