imputeGenosWithMeanPerPop: Genotype imputation

imputeGenosWithMeanPerPopR Documentation

Genotype imputation

Description

Impute missing SNP genotypes with the mean of the non-missing, population by population.

Usage

imputeGenosWithMeanPerPop(
  X,
  pops,
  min.maf.pop = 0.1,
  max.miss.pop = 0.3,
  rm.still.miss = TRUE,
  verbose = 1
)

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

pops

data.frame with 2 columns, "ind" and "pop"

min.maf.pop

minimum minor allele frequency per population (before imputation) below which SNPs are discarded

max.miss.pop

maximum amount of missing genotypes per population (before imputation) above which SNPs are discarded

rm.still.miss

if TRUE, remove SNP(s) still with missing genotype(s) in at least one population (depending on min.maf.pop and max.miss.pop)

verbose

verbosity level (0/1)

Value

matrix with imputed genotypes

Author(s)

Timothee Flutre

See Also

imputeGenosWithMean


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