haplotype_variants {HaploVar}R Documentation

Identify Haplotype Variants

Description

This function requires a VCF and an LD matrix. It will then define local haplotypes and identify the variants for each haplotype. The output can be formatted in six ways, to be compatible with a wide range of GWAS and genomic selection tools.

Usage

haplotype_variants(
  vcf,
  LD,
  epsilon = 0.6,
  MGmin = 30,
  minFreq = 2,
  hetmiss_as = "allele",
  keep_outliers = FALSE,
  format = 1
)

Arguments

vcf

A VCF file.

LD

A LD matrix file.

epsilon

Affects haplotype size. It is a parameter of the DBSCAN clustering tool. The default is 0.6.

MGmin

The minimum number of SNPs within a cluster for it to be defined as a haplotype.The default is 30.

minFreq

The minimum number of individuals a haplotype variant must be present in to be considered a valid haplotype variant. The default is 2.

hetmiss_as

Affects how missing data is handled for all instances where one allele in a genotype is missing.If hetmiss_as = "allele" the genotype is assumed to be heterozygous. If hetmiss_as = "miss" the genotype is treated as NA.

keep_outliers

If FALSE removes SNPs, that are determined to be outliers.

format

The output format. There are six different output formats (1,2,3,4,5,6).

Value

A table of haplotype genotypes in your chosen format.


[Package HaploVar version 0.1.1 Index]