Package: rvHPDT 4.0
rvHPDT: Calling Haplotype-Based and Variant-Based Pedigree Disequilibrium Test for Rare Variants in Pedigrees
To detecting rare variants for binary traits using general pedigrees, the pedigree disequilibrium tests are proposed by collapsing rare haplotypes/variants with/without weights. To run the test, MERLIN is needed in Linux for haplotyping.
Authors:
rvHPDT_4.0.tar.gz
rvHPDT_4.0.zip(r-4.5)rvHPDT_4.0.zip(r-4.4)rvHPDT_4.0.zip(r-4.3)
rvHPDT_4.0.tgz(r-4.4-any)rvHPDT_4.0.tgz(r-4.3-any)
rvHPDT_4.0.tar.gz(r-4.5-noble)rvHPDT_4.0.tar.gz(r-4.4-noble)
rvHPDT_4.0.tgz(r-4.4-emscripten)rvHPDT_4.0.tgz(r-4.3-emscripten)
rvHPDT.pdf |rvHPDT.html✨
rvHPDT/json (API)
| # Install 'rvHPDT' in R: |
| install.packages('rvHPDT', repos = c('https://weiguonimh.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/weiguonimh/rvhpdt/issues
Last updated 2 years agofrom:573d948af8. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 04 2024 |
| R-4.5-win | OK | Nov 04 2024 |
| R-4.5-linux | OK | Nov 04 2024 |
| R-4.4-win | OK | Nov 04 2024 |
| R-4.4-mac | OK | Nov 04 2024 |
| R-4.3-win | OK | Nov 04 2024 |
| R-4.3-mac | OK | Nov 04 2024 |
Exports:convert.factors.to.strings.in.dataframefullPedigreeHapMendlianCheckmydaoshumypasterandomPDTrchildrhapPDTrvPDT.testrvPDT.test.permurvPDT.test.subwhap.prehap
Dependencies:gtools
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert data.frame columns from factors to characters | convert.factors.to.strings.in.dataframe |
| Internal function. | fullPedigree |
| Internal function. | HapMendlianCheck |
| Internal function. | mydaoshu |
| Internal function. | mypaste |
| Internal function. | randomPDT |
| Internal function. | rchild |
| Calling haplotype-based and variant-based pedigree disequilibrium test for rare variants in pedigrees. | rhapPDT |
| Variants-based pedigree disequilibrium test for rare variants in pedigrees. | rvPDT.test |
| Variants-based pedigree disequilibrium test for rare variants in pedigrees. | rvPDT.test.permu |
| Internal function. | rvPDT.test.sub |
| Prepare haplotype pairs for hPDT tests in pedigree data. | whap.prehap |
