imputeGenosWithMean: Genotype imputation

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Genotype imputation

Description

Impute missing SNP genotypes with the mean of the non-missing. The code was inspired from the A.mat function from the rrBLUP package.

Usage

imputeGenosWithMean(X, min.maf = 0.1, max.miss = 0.3, rm.still.miss = TRUE)

Arguments

X	matrix of bi-allelic SNP genotypes encoded in allele doses in 0,1,2, with genotypes in rows and SNPs in columns; missing values should be encoded as NA
min.maf	minimum minor allele frequency (before imputation) below which SNPs are discarded
max.miss	maximum amount of missing genotypes (before imputation) above which SNPs are discarded
rm.still.miss	if TRUE, remove SNP(s) still with missing genotype(s) after imputation (depending on min.maf and max.miss)

Value

matrix with imputed genotypes

Author(s)

Timothee Flutre

See Also

imputeGenosWithMeanPerPop

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.