define_haplotypes

This function requires a VCF and an LD matrix.
It will then define local haplotypes and return a list of tables.
Each table within the list represents one haplotype.
These haplotype tables display the SNP genotypes within the haplotype.

A local haplotyping tool for use in trait association and trait prediction analyses pipelines.
'HaploVar' enables users take single nucleotide polymorphisms (SNPs) (in VCF
format) and a linkage disequilibrium (LD) matrix, calculate local haplotypes and format the
output to be compatible with a wide range of trait association and trait prediction tools.
The local haplotypes are calculated from the LD matrix using a clustering algorithm called
density-based spatial clustering of applications with noise ('DBSCAN') (Ester et al., 1996)
<ISBN: 1577350049>.

Tessa MacNish

HaploVar

Defining Local Haplotype Variants for Use in Trait Association
and Trait Prediction Analyses

Hawlader Al-Mamun

Thomas Bergmann

Mitchell Bestry

Jacob Marsh

David Edwards

define_haplotypes function

<dl><dt>vcf</dt>
<dd>A VCF file.</dd>
<dt>LD</dt>
<dd>A LD matrix file.</dd>
<dt>epsilon</dt>
<dd>Affects haplotype size. It is a parameter of the DBSCAN clustering tool. The default is 0.6.</dd>
<dt>MGmin</dt>
<dd>The minimum number of SNPs within a cluster for it to be defined as a haplotype.The default is 30.</dd>
<dt>hetmiss_as</dt>
<dd>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.</dd>
<dt>keep_outliers</dt>
<dd>If FALSE, removes SNPs that are determined to be outliers.</dd></dl>

Arguments

Define Haplotypes — define_haplotypes

<dl>

<dt>vcf</dt>
<dd>A VCF file.</dd>


<dt>LD</dt>
<dd>A LD matrix file.</dd>


<dt>epsilon</dt>
<dd>Affects haplotype size. It is a parameter of the DBSCAN clustering tool. The default is 0.6.</dd>


<dt>MGmin</dt>
<dd>The minimum number of SNPs within a cluster for it to be defined as a haplotype.The default is 30.</dd>


<dt>hetmiss_as</dt>
<dd>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.</dd>


<dt>keep_outliers</dt>
<dd>If FALSE, removes SNPs that are determined to be outliers.</dd>

</dl>

define_haplotypes: Define Haplotypes

Description

Usage

Value

Arguments