HaploVar: Defining Local Haplotype Variants for Use in Trait Association and Trait Prediction Analyses (original) (raw)

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 ORCID iD [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
NeedsCompilation: no
CRAN checks: HaploVar results

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