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

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>.

Version:	0.1.1
Depends:	R (≥ 4.00)
Imports:	dplyr, tidyr, tibble, magrittr, dbscan
Suggests:	knitr, rmarkdown
Published:	2025-07-21
DOI:	10.32614/CRAN.package.HaploVar
Author:	Tessa MacNish [aut, cre], Hawlader Al-Mamun [ctb], Thomas Bergmann [ctb], Mitchell Bestry [ctb], Jacob Marsh [ctb], David Edwards [ctb]
Maintainer:	Tessa MacNish <tessa.macnish at research.uwa.edu.au>
License:	MIT + file LICENSE
NeedsCompilation:	no
CRAN checks:	HaploVar results

Documentation:

Reference manual:	HaploVar.html , HaploVar.pdf
Vignettes:	introduction (source, R code)

Downloads:

Package source:	HaploVar_0.1.1.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries:	r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): HaploVar_0.1.1.tgz, r-oldrel (x86_64): HaploVar_0.1.1.tgz

Linking:

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