tagphenos() reports the frequency of allele types for each SNP and calculates phenotype associations for the different alleles, before returning this information in a $Varfile in a HapObject. This is an internal function that is not intended for external use.
Arguments
- MGfile
SNP marker groups clustered using DBscan.
- bin_vcf
Binary VCF for region of interest reformatted by run_haplotyping().
- pheno
Input numeric phenotype data for each individual.
- het_phenos
When FALSE, phenotype associations for SNPs are calculated from reference and alternate allele individuals only, when TRUE, heterozygous individuals are included assuming additive allele effects.