zero_one_two_coding: Code genotypes as 0, 1, 2
In StevisonLab/genotypeR: SNP Genotype Marker Design and Analysis

Description Usage Arguments Value Examples

zero_one_two_coding code homozygous reference as 0, heterozygous as 1, and homozygous alternate as 2 using a genotypeR object created with initialize_genotypeR_data with the pass_through argument.

1	zero_one_two_coding(genotype_warnings_passthrough, genotype_table)

`genotype_warnings_passthrough`	is a genotypeR object that has been processed by BC_Genotype_Warnings with output="pass_through"
`genotype_table`	is a data frame produced with Ref_Alt_Table

A data frame of 0, 1, and 2 coded genotypes as a slot in the input

data(genotypes_data)
data(markers)
## genotype table
marker_names <- make_marker_names(markers)
GT_table <- Ref_Alt_Table(marker_names)
## remove those markers that did not work
genotypes_data_filtered <- genotypes_data[,c(1, 2, grep("TRUE",
colnames(genotypes_data)%in%GT_table$marker_names))]

pass_through <- initialize_genotypeR_data(seq_data = genotypes_data_filtered,
genotype_table = GT_table, output = "pass_through")

genotypes_object <- zero_one_two_coding(pass_through, GT_table)