Package: CJAMP 0.1.1
CJAMP: Copula-Based Joint Analysis of Multiple Phenotypes
We provide a computationally efficient and robust implementation of the recently proposed C-JAMP (Copula-based Joint Analysis of Multiple Phenotypes) method (Konigorski et al., 2019, submitted). C-JAMP allows estimating and testing the association of one or multiple predictors on multiple outcomes in a joint model, and is implemented here with a focus on large-scale genome-wide association studies with two phenotypes. The use of copula functions allows modeling a wide range of multivariate dependencies between the phenotypes, and previous results are supporting that C-JAMP can increase the power of association studies to identify associated genetic variants in comparison to existing methods (Konigorski, Yilmaz, Pischon, 2016, <doi:10.1186/s12919-016-0045-6>; Konigorski, Yilmaz, Bull, 2014, <doi:10.1186/1753-6561-8-S1-S72>). In addition to the C-JAMP functions, functions are available to generate genetic and phenotypic data, to compute the minor allele frequency (MAF) of genetic markers, and to estimate the phenotypic variance explained by genetic markers.
Authors:
CJAMP_0.1.1.tar.gz
CJAMP_0.1.1.zip(r-4.5)CJAMP_0.1.1.zip(r-4.4)CJAMP_0.1.1.zip(r-4.3)
CJAMP_0.1.1.tgz(r-4.4-any)CJAMP_0.1.1.tgz(r-4.3-any)
CJAMP_0.1.1.tar.gz(r-4.5-noble)CJAMP_0.1.1.tar.gz(r-4.4-noble)
CJAMP_0.1.1.tgz(r-4.4-emscripten)CJAMP_0.1.1.tgz(r-4.3-emscripten)
CJAMP.pdf |CJAMP.html✨
CJAMP/json (API)
| # Install 'CJAMP' in R: |
| install.packages('CJAMP', repos = c('https://skonigor.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 6 years agofrom:ad7c345200. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 09 2024 |
| R-4.5-win | WARNING | Sep 09 2024 |
| R-4.5-linux | WARNING | Sep 09 2024 |
| R-4.4-win | WARNING | Sep 09 2024 |
| R-4.4-mac | WARNING | Sep 09 2024 |
| R-4.3-win | WARNING | Sep 09 2024 |
| R-4.3-mac | WARNING | Sep 09 2024 |
Exports:cjampcjamp_loopcompute_expl_varcompute_MAFgenerate_clayton_copulagenerate_doubleton_datagenerate_genodatagenerate_phenodata_1generate_phenodata_1_simplegenerate_phenodata_2_bvngenerate_phenodata_2_copulagenerate_singleton_dataget_estimates_naivelrt_copulalrt_paramminusloglik
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| C-JAMP: Copula-based joint analysis of multiple phenotypes. | cjamp cjamp_loop |
| Phenotypic variance explained by genetic variants. | compute_expl_var |
| Compute minor allele frequency of genetic variants. | compute_MAF |
| Generate data from the Clayton copula. | generate_clayton_copula |
| Functions to generate genetic data. | generate_doubleton_data generate_genodata generate_singleton_data |
| Functions to generate phenotype data. | generate_phenodata generate_phenodata_1 generate_phenodata_1_simple generate_phenodata_2_bvn generate_phenodata_2_copula |
| Naive estimates of the copula and marginal parameters. | get_estimates_naive |
| Compute likelihood ratio tests. | lrt lrt_copula lrt_param |
| Minus log-likelihood of copula models. | minusloglik |
| Summary function. | summary.cjamp |
