Introduction | Preparing inputs | Define Haplotypes | Collate Define Haplotypes | Define Haplotypes Globally | Identify Haplotypes Variants | Collate Haplotypes Variants | Identify Haplotypes Variants Globally | References
Package: HaploVar 0.1.2
Tessa MacNish
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>.
Authors:
HaploVar_0.1.2.tar.gz
HaploVar_0.1.2.zip(r-4.7-any)HaploVar_0.1.2.zip(r-4.6-any)HaploVar_0.1.2.zip(r-4.5-any)
HaploVar_0.1.2.tgz(r-4.6-any)HaploVar_0.1.2.tgz(r-4.5-any)
HaploVar_0.1.2.tar.gz(r-4.7-any)HaploVar_0.1.2.tar.gz(r-4.6-any)
HaploVar_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HaploVar/json (API)
| # Install 'HaploVar' in R: |
| install.packages('HaploVar', repos = c('https://tessamacnish.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tessamacnish/haplovar/issues
Last updated from:696c45c67d. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 124 | ||
| source / vignettes | OK | 2355 | ||
| linux-release | OK | 107 | ||
| macos-release | OK | 103 | ||
| macos-oldrel | OK | 98 | ||
| windows-devel | OK | 84 | ||
| windows-release | OK | 87 | ||
| windows-oldrel | OK | 76 | ||
| wasm-release | OK | 88 |
Exports:collate_define_haplotypescollate_haplotype_variantsdefine_haplotypesdefine_haplotypes_globallyhaplotype_variantshaplotype_variants_global
Dependencies:clicpp11dbscandplyrgenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Collate define_haplotypes Lists | collate_define_haplotypes |
| Collate haplotype_variants Tables | collate_haplotype_variants |
| Define Haplotypes | define_haplotypes |
| Define Haplotypes Globally | define_haplotypes_globally |
| Identify Haplotype Variants | haplotype_variants |
| Identify Haplotype Variants Globally | haplotype_variants_global |
| Linkage Disequilibrium Matrix | LD |
| Brassica napus genotype data in VCF format | vcf |