run_hdbscan_haplotyping: Cluster SNPs with HDBSCAN and identify haplotypes

In crosshap: Local Haplotype Clustering and Visualization

Cluster SNPs with HDBSCAN and identify haplotypes

Description

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).

Usage

run_hdbscan_haplotyping(
  vcf,
  LD,
  pheno,
  MGmin,
  minHap = 5,
  hetmiss_as = "allele",
  metadata = NULL,
  keep_outliers = FALSE
)

Arguments

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

Value

A comprehensive haplotyping S3 object (HapObject) for each provided epsilon value, needed for clustree_viz() and crosshap_viz().

crosshap documentation built on May 29, 2024, 1:13 a.m.