Fill in missing values in SnpMatrix object

Uses snpStats' snp.imputation function

impute.missing(X, bp = 1:ncol(X), strata = NULL, numeric = FALSE, ...)

Arguments

X

SnpMatrix object
bp

optional vector of base pair positions, length == number of SNPs
strata

optional vector, length == number of samples, as.factor(strata) defines distinct strata of samples, eg by geography
numeric

default FALSE
...

arguments passed on to impute.snps

Value

matrix, either numeric (if numeric=TRUE) or SnpMatrix (if numeric=FALSE)