haplotype_variants_global {HaploVar}R Documentation

Identify Haplotype Variants Globally

Description

This function requires a list of VCF files and an LD matrices. 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_global(
  vcf_list,
  LD_list,
  epsilon = NULL,
  MGmin = 30,
  minFreq = 2,
  hetmiss_as = "allele",
  keep_outliers = FALSE,
  format = 1
)

Arguments

vcf_list

A list of VCF files.

LD_list

A list of LD matrix files.

epsilon

A list of epsilon values the same length as the list of VCF files. The 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]