Description Usage Arguments Value Examples
binary_coding
codes genotypes contained in a genotypeR object
and places them into a genotypeR object's binary_genotype slot.
1 | binary_coding(genotype_warnings2NA, genotype_table)
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genotype_warnings2NA |
this is a genotypeR object that has been through BC_Genotype_Warnings with either output="warnings2NA" or output="pass_through" |
genotype_table |
this is a marker table produced with Ref_Alt_Table |
A data frame of binary coded genotypes as a slot in the genotypeR input genotype_warnings2NA
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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))]
warnings_out2NA <- initialize_genotypeR_data(seq_data = genotypes_data_filtered,
genotype_table = GT_table, output = "warnings2NA")
genotypes_object <- binary_coding(warnings_out2NA, GT_table)
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