<p>Pairwise R^2 values for 490 Brassica napus single nucleotide polymorphisms (SNPs).</p>

datasets

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

LD function

<p>An object of class <code>data.frame</code> with 490 rows and 490 columns.</p>

Format

Linkage Disequilibrium Matrix — LD

Linkage Disequilibrium Matrix

LD: Linkage Disequilibrium Matrix

Description

Usage

Arguments

Format