impute_genotypes: impute missing genotypes based on pop structure characterised...

In pygmyperch/melfuR: A collection of ugly R functions for analysis of SNP and spatial data.

impute missing genotypes based on pop structure characterised using snmf

Description

impute missing genotypes based on pop structure characterised using snmf

Usage

impute_genotypes(input.genotypes, K = NULL, no_cores = 1)

Arguments

input.genotypes	A genind or genlight object
K	the number of predetermined clusters in your data (suggest using smnf, ADMIXTURE or similar to explore first)
no_cores	the number of cores to use for the analysis

Value

a genind or genlight object with missing data imputed

#' @details The function imputes missing genotypes based on ancestral population allele frequencies estimated using LEA::snmf()

Author(s)

Chris Brauer

Examples

 ## set directory for results to be written
 setwd("path/to/working/directory")

 # load example coordinate file
 data(rainbow.genind)

 # run analysis for K=6
 imputed.gi <- impute_genotypes(rainbow.genind, K = 6)
 

pygmyperch/melfuR documentation built on Aug. 26, 2024, 12:48 a.m.