Impute missing genotypes

Description

Impute missing genotypes in a snpMatrix object in each SNP in turn, conditional on all the others.

Usage

1
  fillin(X, bp = 1:ncol(X), strata = NULL)

Arguments

X

a snpMatrix object

bp

optional vector giving basepair positions of the SNPs

strata

optional vector giving stratificiation of the samples, one entry for each sample, and samples with the same value are assumed to come from a single strata

Value

a numeric matrix of imputed genotypes, 0,2 = homs, 1 = het


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