impute_missing_genotypes: Impute missing genotypes

In FellouMada/rSNPdata: R package for Analysis of P. falciparum whole genome SNPs data

Impute missing genotypes

Description

missing genotype imputation based on the MAF at any given locus. Imputation will be done nsim times and imputed data with highest correlation between MAF from raw data and MAF from imputed data will be retained

Usage

snpdata = impute_missing_genotypes(snpdata)

Arguments

snpdata	a SNPdata object
genotype	the genotype table from which the missing data will be imputed
nsim	an integer. the number of simulations

Details

when both alleles are not supported by any read or the total number of reads supporting both alleles at a given site is < 5, the genotype will be phased based on a bernouli distribition using the MAF as a parameter. Similarly, when the total number of reads is > 5 and the number of reads supporting one of the allele is not 2 times the number of the other allele, the genotype is phased using a bernouli distribution

Value

a SNPdata object with an additional table named as "Phased_Imputed"

FellouMada/rSNPdata documentation built on June 12, 2022, 7:29 p.m.