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Impute missing genotypes

Source: R/AllGenerics.R, R/qc.R
imputeMarkers.Rd

Fills missing dosages with twice the allele frequency of the marker, the simple mean imputation that relationship matrices assume. It is adequate for the low rates of missingness left after quality control; for anything more, impute with dedicated software before building the object.

Usage

imputeMarkers(x, ...)

# S4 method for class 'BreedingExperiment'
imputeMarkers(x, ...)

Arguments

x

A BreedingExperiment object.

...

Unused.

Value

A BreedingExperiment object with no missing genotypes.

See also

filterMarkers()

Examples

set.seed(1)
be <- simulateBreeding(n_ind = 20, n_marker = 50, missing = 0.1)
anyNA(genotypes(be))
#> [1] TRUE
anyNA(genotypes(imputeMarkers(be)))
#> [1] FALSE