Introduction | Preparing inputs | Define Haplotypes | Collate Define Haplotypes | Define Haplotypes Globally | Identify Haplotypes Variants | Collate Haplotypes Variants | Identify Haplotypes Variants Globally | References
Package: HaploVar 0.1.1
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_0.1.1.tar.gz
HaploVar_0.1.1.zip(r-4.7)HaploVar_0.1.1.zip(r-4.6)HaploVar_0.1.1.zip(r-4.5)
HaploVar_0.1.1.tgz(r-4.6-any)HaploVar_0.1.1.tgz(r-4.5-any)
HaploVar_0.1.1.tar.gz(r-4.7-any)HaploVar_0.1.1.tar.gz(r-4.6-any)
HaploVar_0.1.1.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://t-macnish.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:7402a12912. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 108 | ||
| source / vignettes | OK | 264 | ||
| linux-release-x86_64 | OK | 119 | ||
| macos-release-arm64 | OK | 139 | ||
| macos-oldrel-arm64 | OK | 193 | ||
| windows-devel | OK | 83 | ||
| windows-release | OK | 94 | ||
| windows-oldrel | OK | 81 | ||
| wasm-release | OK | 108 |
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 |
