recode_snps: Recode genotypic data
In mwesthues/sspredr: Single-Step Prediction

Description Usage Arguments Value Examples

recode_snps recodes the elements of a SNP-matrix

1 2	recode_snps(x, major, minor, major_coding, minor_coding, het_coding, missing_value, na_coding)

`x`	A matrix. Genotype names are stored in rows whereas marker names are stored in columns.
`major`	Character vector with names of major genotype at each locus.
`minor`	Character vector with names of minor genotype at each locus.
`major_coding`	Scalar specifying how to recode the major genotype.
`minor_coding`	Scalar specifying how to recode the minor genotype.
`het_coding`	Scalar specifying how to recode heterozygous loci.
`missing_value`	Scalar specifying how missing values are encoded in `x`.
`na_coding`	Scalar specifying how to recode missing values.

A matrix with the same dimensions as x but with recoded SNP genotypes.

 # First, determine the major and minor allele at each locus of SNP-genotypes
 geno_lst <- compute_maf(marker_character, output = "geno_list",
                         missing_value = "??", maf_threshold = 0)
 major <- geno_lst[["major_genotype"]]
 minor <- geno_lst[["minor_genotype"]]

 # Recode the major allele as '2', the minor allele as '0' and heterozygotes
 # as '0'.
 recode_snps(marker_character, major = major, minor = minor,
             major_coding = 2, minor_coding = 0, het_coding = 1,
             missing_value = "??", na_coding = NA_real_)