Package: mlmm.gwas 1.0.6
Clement Mabire
mlmm.gwas: Pipeline for GWAS Using MLMM
Pipeline for Genome-Wide Association Study using Multi-Locus Mixed Model from Segura V, Vilhjálmsson BJ et al. (2012) <doi:10.1038/ng.2314>. The pipeline include detection of associated SNPs with MLMM, model selection by lowest eBIC and p-value threshold, estimation of the effects of the SNPs in the selected model and graphical functions.
Authors:
mlmm.gwas_1.0.6.tar.gz
mlmm.gwas_1.0.6.tar.gz(r-4.5-noble)mlmm.gwas_1.0.6.tar.gz(r-4.4-noble)
mlmm.gwas_1.0.6.tgz(r-4.4-emscripten)mlmm.gwas_1.0.6.tgz(r-4.3-emscripten)
mlmm.gwas.pdf |mlmm.gwas.html✨
mlmm.gwas/json (API)
NEWS
| # Install 'mlmm.gwas' in R: |
| install.packages('mlmm.gwas', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- K.add - Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
- K.dom - Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
- K.female - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
- K.hybrid - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
- K.male - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
- Xa - Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
- Xd - Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
- Xf - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
- Xfm - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
- Xm - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
- female - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
- floweringDateAD - Dataset for examples with the mlmm.gwas package, additive and additive+dominance models
- floweringDateFMI - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
- hybrid - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
- male - Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:343107cb65. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 23 2024 |
| R-4.5-linux | OK | Aug 23 2024 |
Exports:eBIC_allmodelsEstimation_allmodelsfromeBICtoEstimationfrommlmm_toebicgenotypes.boxplotmanhattan.plotmlmm_allmodelsrun_entire_gwas_pipelinethreshold_allmodels
Dependencies:bdsmatrixcodetoolscoxmecrayonlatticeMASSMatrixmultcompmultcompViewmvtnormnlmeRcppRcppArmadilloRcppProgresssandwichsommersurvivalTH.datazoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute eBIC and BIC criteria | eBIC_allmodels |
| Compute estimated effects | Estimation_allmodels |
| Helper function that create the selec_XXclass argument of the Estimation_allmodels function | fromeBICtoEstimation |
| Helper that create the selec_XX argument of eBIC_allmodels() | frommlmm_toebic |
| Boxplots representation of the distributions of phenotypes according to allelic classes | genotypes.boxplot |
| Manhattan plot | manhattan.plot |
| Multi-Locus Mixed-Model | mlmm_allmodels |
| mlmm.gwas | mlmm.gwas-package mlmm.gwas |
| Dataset for examples with the mlmm.gwas package, additive and additive+dominance models | floweringDateAD K.add K.dom mlmm.gwas.AD Xa Xd |
| Dataset for examples with the mlmm.gwas package, male+female and male+female+interaction models | female floweringDateFMI hybrid K.female K.hybrid K.male male mlmm.gwas.FMI Xf Xfm Xm |
| MLMM, model selection and effects estimation | run_entire_gwas_pipeline |
| Select significant marker thanks to a p-value threshold | threshold_allmodels |