tagphenos {crosshap}

Calculate SNP phenotypic associations

Description

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.

Usage

tagphenos(MGfile, bin_vcf, pheno, het_phenos = FALSE)

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.

Value

Returns intermediate of haplotype object.