Package: mvMAPIT 2.0.3
mvMAPIT: Multivariate Genome Wide Marginal Epistasis Test
Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants that are involved in epistasis, and nearly all of these approaches carry out this task by focusing on analyzing one trait at a time. Previous studies have shown that jointly modeling multiple phenotypes can often dramatically increase statistical power for association mapping. In this package, we present the 'multivariate MArginal ePIstasis Test' ('mvMAPIT') – a multi-outcome generalization of a recently proposed epistatic detection method which seeks to detect marginal epistasis or the combined pairwise interaction effects between a given variant and all other variants. By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact – thus, potentially alleviating much of the statistical and computational burden associated with conventional explicit search based methods. Our proposed 'mvMAPIT' builds upon this strategy by taking advantage of correlation structure between traits to improve the identification of variants involved in epistasis. We formulate 'mvMAPIT' as a multivariate linear mixed model and develop a multi-trait variance component estimation algorithm for efficient parameter inference and P-value computation. Together with reasonable model approximations, our proposed approach is scalable to moderately sized genome-wide association studies. Crawford et al. (2017) <doi:10.1371/journal.pgen.1006869>. Stamp et al. (2023) <doi:10.1093/g3journal/jkad118>.
Authors:
mvMAPIT_2.0.3.tar.gz
mvMAPIT_2.0.3.tar.gz(r-4.5-noble)mvMAPIT_2.0.3.tar.gz(r-4.4-noble)
mvMAPIT.pdf |mvMAPIT.html✨
mvMAPIT/json (API)
NEWS
# Install 'mvMAPIT' in R: |
install.packages('mvMAPIT', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lcrawlab/mvmapit/issues
Pkgdown:https://lcrawlab.github.io
- mvmapit_data - Multivariate MAPIT analysis and exhaustive search analysis.
- phillips_data - Multivariate MAPIT analysis of binding affinities in broadly neutralizing antibodies.
- simulated_data - Genotype and trait data with epistasis.
Last updated 1 years agofrom:0eada31faf. Checks:OK: 1 NOTE: 1. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 23 2024 |
R-4.5-linux-x86_64 | NOTE | Nov 23 2024 |
Exports:cauchy_combinedfishers_combinedharmonic_combinedmvmapitsimulate_traits
Dependencies:backportsbriocallrcheckmateclicodetoolsCompQuadFormcpp11crayondescdiffobjdigestdplyrevaluatefansiFMStableforeachfsgenericsglueharmonicmeanpiteratorsjsonlitelifecycleloggingmagrittrmvtnormpillarpkgbuildpkgconfigpkgloadpraiseprocessxpspurrrR6RcppRcppArmadilloRcppParallelRcppProgressRcppSpdlogrlangrprojrootstringistringrtestthattibbletidyrtidyselectutf8vctrswaldowithr
Dockerized mvMAPIT
Rendered fromtutorial-docker-mvmapit.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2022-12-05
Started: 2022-12-05
Empirical comparison of P-value combination methods in mvMAPIT
Rendered fromstudy-compare-p-value-combine-methods.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2023-09-22
Started: 2023-09-22
Illustrating multivariate MAPIT with Simulated Data
Rendered frommvMAPIT.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2023-09-22
Started: 2022-12-05
Joint modeling of hematology traits yields epistatic signal in stock of mice
Rendered fromstudy-wtccc-mice.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2023-09-22
Started: 2022-12-05
Simulate Traits
Rendered fromtutorial-simulations.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2022-12-05
Started: 2022-12-05
Synergistic epistasis in binding affinity landscapes
Rendered fromstudy-phillips-bnabs.Rmd
usingknitr::rmarkdown
on Nov 23 2024.Last update: 2022-12-05
Started: 2022-12-05
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Cauchy p combine method on mvmapit return | cauchy_combined |
Fisher's combine method on mvmapit return | fishers_combined |
Harmonic mean p combine method on mvmapit return | harmonic_combined |
Multivariate MArginal ePIstasis Test (mvMAPIT) | mvmapit |
Multivariate MAPIT analysis and exhaustive search analysis. | mvmapit_data |
Multivariate MAPIT analysis of binding affinities in broadly neutralizing antibodies. | phillips_data |
Simulate phenotye data | simulate_traits |
Genotype and trait data with epistasis. | simulated_data |