run_hdbscan_haplotyping

run_hdbscan_haplotyping() performs HDBSCAN clustering of SNPs in region of
interest to identify marker groups. Individuals are classified by haplotype
combination based on shared combinations of marker group alleles. Returns a
comprehensive haplotyping object (HapObject), which can be visualized with reference
to phenotype and metadata using crosshap_viz() (set epsilon to 1 as a dummy value).

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

run_hdbscan_haplotyping function

<dl><dt>vcf</dt>
<dd>Input VCF for region of interest.</dd>
<dt>LD</dt>
<dd>Pairwise correlation matrix of SNPs in region (e.g. from PLINK).</dd>
<dt>pheno</dt>
<dd>Input numeric phenotype data for each individual.</dd>
<dt>MGmin</dt>
<dd>Minimum SNPs in marker groups, MinPts parameter for DBscan.</dd>
<dt>minHap</dt>
<dd>Minimum nIndividuals in a haplotype combination.</dd>
<dt>hetmiss_as</dt>
<dd>If hetmiss_as = "allele", heterozygous-missing SNPs './N'
are recoded as 'N/N', if hetmiss_as = "miss", the site is recoded as missing.</dd>
<dt>metadata</dt>
<dd>Metadata input (optional).</dd>
<dt>keep_outliers</dt>
<dd>When FALSE, marker group smoothing is performed to
remove outliers.</dd></dl>

Arguments

Cluster SNPs with HDBSCAN and identify haplotypes — run_hdbscan_haplotyping

<dl>

<dt>vcf</dt>
<dd>Input VCF for region of interest.</dd>


<dt>LD</dt>
<dd>Pairwise correlation matrix of SNPs in region (e.g. from PLINK).</dd>


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


<dt>MGmin</dt>
<dd>Minimum SNPs in marker groups, MinPts parameter for DBscan.</dd>


<dt>minHap</dt>
<dd>Minimum nIndividuals in a haplotype combination.</dd>


<dt>hetmiss_as</dt>
<dd>If hetmiss_as = "allele", heterozygous-missing SNPs './N'
are recoded as 'N/N', if hetmiss_as = "miss", the site is recoded as missing.</dd>


<dt>metadata</dt>
<dd>Metadata input (optional).</dd>


<dt>keep_outliers</dt>
<dd>When FALSE, marker group smoothing is performed to
remove outliers.</dd>

</dl>

run_hdbscan_haplotyping: Cluster SNPs with HDBSCAN and identify haplotypes

Description

Usage

Value

Arguments