Overview | Writing gemma2 | Algorithmic differences from Zhou's GEMMA | Comparing Zhou's GEMMA (v0.96) EM output with that of gemma2 | Running gemma2 with example data | Direct comparison of GEMMA results with those of gemma2 | References
Package: gemma2 0.1.3
gemma2: GEMMA Multivariate Linear Mixed Model
Fits a multivariate linear mixed effects model that uses a polygenic term, after Zhou & Stephens (2014) (<https://www.nature.com/articles/nmeth.2848>). Of particular interest is the estimation of variance components with restricted maximum likelihood (REML) methods. Genome-wide efficient mixed-model association (GEMMA), as implemented in the package 'gemma2', uses an expectation-maximization algorithm for variance components inference for use in quantitative trait locus studies.
Authors:
gemma2_0.1.3.tar.gz
gemma2_0.1.3.zip(r-4.7-any)gemma2_0.1.3.zip(r-4.6-any)gemma2_0.1.3.zip(r-4.5-any)
gemma2_0.1.3.tgz(r-4.6-any)gemma2_0.1.3.tgz(r-4.5-any)
gemma2_0.1.3.tar.gz(r-4.7-any)gemma2_0.1.3.tar.gz(r-4.6-any)
gemma2_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gemma2/json (API)
| # Install 'gemma2' in R: |
| install.packages('gemma2', repos = c('https://fboehm.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fboehm/gemma2/issues
em-algorithmgeneticsmixed-models
Last updated from:ea3052f860. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 145 | ||
| source / vignettes | OK | 323 | ||
| linux-release | NOTE | 128 | ||
| macos-release | NOTE | 168 | ||
| macos-oldrel | NOTE | 192 | ||
| windows-devel | NOTE | 89 | ||
| windows-release | NOTE | 56 | ||
| windows-oldrel | NOTE | 82 | ||
| wasm-release | OK | 110 |
Exports:calc_omegacalc_qicalc_XHiYcenter_kinshipeigen_proceigen2MphEMstagger_matsupdate_u
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate Omega matrices | calc_omega |
| Calculate Qi (inverse of Q) and log determinant of Q | calc_qi |
| Calculate Sigma_ee and Sigma_uu matrices | calc_sigma |
| Calculate XHiY | calc_XHiY |
| Center a relatedness matrix, after Zhou's GEMMA function CenterMatrix | center_kinship |
| Eigendecomposition procedure for Vg and Ve | eigen_proc |
| Calculate eigendecomposition and return ordered eigenvalues and eigenvectors | eigen2 |
| gemma2 | gemma2 |
| Calculate log likelihood | MphCalcLogL |
| Perform expectation-maximization algorithm to infer Vg and Ve values for a pair of traits. | MphEM |
| Stagger matrices within a larger, block-diagonal matrix | stagger_mats |
| Update E | update_e |
| Update U matrix | update_u |
| Update V_e and V_g | update_v |
| Update B for restricted log likelihood | UpdateRL_B |