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:
Downloads:
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