run_hdbscan_haplotyping {crosshap} | R Documentation |
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().