tagphenos

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.

A local haplotyping visualization toolbox to capture major patterns
of co-inheritance between clusters of linked variants, whilst connecting findings
to phenotypic and demographic traits across individuals. 'crosshap' enables users
to explore and understand genomic variation across a trait-associated region.
For an example of successful local haplotype analysis, see Marsh et al. (2022)
<doi:10.1007/s00122-022-04045-8>.

Jacob Marsh

crosshap

Local Haplotype Clustering and Visualization

Brady Johnston

Jakob Petereit

tagphenos function

<dl><dt>MGfile</dt>
<dd>SNP marker groups clustered using DBscan.</dd>
<dt>bin_vcf</dt>
<dd>Binary VCF for region of interest reformatted by
run_haplotyping().</dd>
<dt>pheno</dt>
<dd>Input numeric phenotype data for each individual.</dd>
<dt>het_phenos</dt>
<dd>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.</dd></dl>

Arguments

Calculate SNP phenotypic associations — tagphenos

<dl>

<dt>MGfile</dt>
<dd>SNP marker groups clustered using DBscan.</dd>


<dt>bin_vcf</dt>
<dd>Binary VCF for region of interest reformatted by
run_haplotyping().</dd>


<dt>pheno</dt>
<dd>Input numeric phenotype data for each individual.</dd>


<dt>het_phenos</dt>
<dd>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.</dd>

</dl>

tagphenos: Calculate SNP phenotypic associations

Description

Usage

Value

Arguments