Package: csmGmm 0.4.0
csmGmm: Conditionally Symmetric Multidimensional Gaussian Mixture Model
Implements the conditionally symmetric multidimensional Gaussian mixture model (csmGmm) for large-scale testing of composite null hypotheses in genetic association applications such as mediation analysis, pleiotropy analysis, and replication analysis. In such analyses, we typically have J sets of K test statistics where K is a small number (e.g. 2 or 3) and J is large (e.g. 1 million). For each one of the J sets, we want to know if we can reject all K individual nulls. Please see the vignette for a quickstart guide. The paper describing these methods is "Testing a Large Number of Composite Null Hypotheses Using Conditionally Symmetric Multidimensional Gaussian Mixtures in Genome-Wide Studies" by Sun R, McCaw Z, & Lin X (Journal of the American Statistical Association 2025, <doi:10.1080/01621459.2024.2422124>).
Authors:
csmGmm_0.4.0.tar.gz
csmGmm_0.4.0.zip(r-4.7)csmGmm_0.4.0.zip(r-4.6)csmGmm_0.4.0.zip(r-4.5)
csmGmm_0.4.0.tgz(r-4.6-any)csmGmm_0.4.0.tgz(r-4.5-any)
csmGmm_0.4.0.tar.gz(r-4.7-any)csmGmm_0.4.0.tar.gz(r-4.6-any)
csmGmm_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
csmGmm/json (API)
| # Install 'csmGmm' in R: |
| install.packages('csmGmm', repos = c('https://ryansunwork.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 from:35f116a0ea. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 142 | ||
| source / vignettes | OK | 234 | ||
| linux-release-x86_64 | OK | 142 | ||
| macos-release-arm64 | OK | 104 | ||
| macos-oldrel-arm64 | OK | 135 | ||
| windows-devel | OK | 92 | ||
| windows-release | OK | 106 | ||
| windows-oldrel | OK | 96 | ||
| wasm-release | OK | 100 |
Exports:calc_dens_corcalc_dens_ind_2dcalc_dens_ind_3dcalc_dens_ind_multiplecheck_incongruousfind_2dfind_3dfind_max_meanssymm_fit_cor_EMsymm_fit_cor_EM_fullliksymm_fit_cor_EM_noAssumptionsymm_fit_cor_EM_rhosymm_fit_ind_EMsymm_fit_ind_EM_noAssumption
Dependencies:clidplyrgenericsgluelifecyclemagrittrmvtnormpillarpkgconfigR6rlangtibbletidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calc_dens_cor.R | calc_dens_cor |
| calc_dens_ind.R | calc_dens_ind_2d |
| Calculate J trivariate normal densities (all dimensions are independent) under fitted csmGmm. | calc_dens_ind_3d |
| Calculate the density of K-dimensional multivariate normal (all dimensions are independent) under fitted acsGmm. | calc_dens_ind_multiple |
| check_incongruous.R | check_incongruous |
| Tells if row x if allTestStats is an incongruous result (has a higher lfdr than a set of test statistics with lower magnitudes). For K=2 case. | find_2d |
| Tells if row x if allTestStats is an incongruous result (has a higher lfdr than a set of test statistics with lower magnitudes). For K=3 case. | find_3d |
| find_max_means.R | find_max_means |
| symm_fit_cor.R | symm_fit_cor_EM |
| symm_fit_cor_fulllik.R | symm_fit_cor_EM_fulllik |
| symm_fit_cor_noAssumption.R | symm_fit_cor_EM_noAssumption |
| symm_fit_cor_rho.R | symm_fit_cor_EM_rho |
| symm_fit_ind.R | symm_fit_ind_EM |
| symm_fit_ind_noAssumption.R | symm_fit_ind_EM_noAssumption |
