Introduction and Background | Statistical Description | Using hapassoc and its features | Examples | Summary
Package: hapassoc 1.2-9
hapassoc: Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.
Authors:
hapassoc_1.2-9.tar.gz
hapassoc_1.2-9.zip(r-4.7-x86_64)hapassoc_1.2-9.zip(r-4.7-arm64)hapassoc_1.2-9.zip(r-4.6-x86_64)hapassoc_1.2-9.zip(r-4.6-arm64)hapassoc_1.2-9.zip(r-4.5-x86_64)
hapassoc_1.2-9.tgz(r-4.6-x86_64)hapassoc_1.2-9.tgz(r-4.6-arm64)hapassoc_1.2-9.tgz(r-4.5-x86_64)hapassoc_1.2-9.tgz(r-4.5-arm64)
hapassoc_1.2-9.tar.gz(r-4.7-arm64)hapassoc_1.2-9.tar.gz(r-4.7-x86_64)hapassoc_1.2-9.tar.gz(r-4.6-arm64)hapassoc_1.2-9.tar.gz(r-4.6-x86_64)
hapassoc_1.2-9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
hapassoc/json (API)
| # Install 'hapassoc' in R: |
| install.packages('hapassoc', repos = c('https://kmburkett.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sfustatgen/research/issues
Datasets:
- hypoDat - Simulated data for a hypothetical binary trait
- hypoDatGeno - Simulated data for a hypothetical genetic SNPs
Last updated from:e844507d05. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 78 | ||
| linux-devel-x86_64 | OK | 91 | ||
| source / vignettes | OK | 160 | ||
| linux-release-arm64 | OK | 72 | ||
| linux-release-x86_64 | OK | 110 | ||
| macos-release-arm64 | OK | 114 | ||
| macos-release-x86_64 | OK | 333 | ||
| macos-oldrel-arm64 | OK | 103 | ||
| macos-oldrel-x86_64 | OK | 373 | ||
| windows-devel-arm64 | OK | 327 | ||
| windows-devel-x86_64 | OK | 97 | ||
| windows-release-arm64 | OK | 328 | ||
| windows-release-x86_64 | OK | 58 | ||
| windows-oldrel-x86_64 | OK | 63 | ||
| wasm-release | OK | 63 |
Exports:hapassocpre.hapassoc
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Return likelihood ratio test of haplotype effect | anova.hapassoc |
| EM algorithm to fit maximum likelihood estimates of trait associations with SNP haplotypes | hapassoc |
| Simulated data for a hypothetical binary trait | hypoDat |
| Simulated data for a hypothetical genetic SNPs | hypoDatGeno |
| Return log-likelihood | logLik.hapassoc |
| Pre-process the data before fitting it with hapassoc | pre.hapassoc |
| Summarize results of the hapassoc function | summary.hapassoc |