Recode genotypes

Returns a recoded genoMatrix object, genetic model, imputation, and weights can be recoded.

recode(object, geneticModel, imputeMethod, weights, MAFweights)

Arguments

object

An object of class genoMatrix

geneticModel

Accepted values include "allelic", "dominant", "recessive".

imputeMethod

Logic for recoding of missing genotypes. The default, "meanImpute" recodes NA to the mean genotype dosage. "missingToRef" recodes NA to 0.

weights

A vector of weights, with length equal to the number of variants.

MAFweights

Apply MAF-dependent weighting, current options include "none" and "mb" (Madsen-Browning).