merge_impute: Merge two genotype matrices and impute missing data...

In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

Merge two genotype matrices and impute missing data (deprecated)

Description

Merge two genotype matrices and impute missing data by BLUP

Usage

merge_impute(geno1, geno2, ploidy)

Arguments

geno1	Genotype matrix (coded 0...ploidy) with dimensions markers x indiv
geno2	Genotype matrix (coded 0...ploidy) with dimensions markers x indiv
ploidy	Either 2 or 4

Details

This function is obsolete. Use impute_L2H instead.

Designed to impute from low to high density markers. The BLUP method is equivalent to Eq. 4 of Poland et al. (2012), but this function is not iterative. Additional shrinkage toward the mean is applied if needed to keep the imputed values within the range [0,ploidy]. Missing data in the input matrices are imputed with the population mean for each marker. If an individual appears in both input matrices, it is renamed with suffixes ".1" and ".2" and treated as two different individuals. Monomorphic markers are removed.

Value

Imputed genotype matrix (markers x indiv)

References

Poland et al. (2012) Plant Genome 5:103-113.

jendelman/polyBreedR documentation built on Jan. 5, 2025, 12:13 a.m.