Package: depower 2024.12.4.999
depower: Power Analysis for Differential Expression Studies
Provides a convenient framework to simulate, test, power, and visualize data for differential expression studies with lognormal or negative binomial outcomes. Supported designs are two-sample comparisons of independent or dependent outcomes. Power may be summarized in the context of controlling the per-family error rate or family-wise error rate. Negative binomial methods are described in Yu, Fernandez, and Brock (2017) <doi:10.1186/s12859-017-1648-2> and Yu, Fernandez, and Brock (2020) <doi:10.1186/s12859-020-3541-7>.
Authors:
depower_2024.12.4.999.tar.gz
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depower.pdf |depower.html✨
depower/json (API)
NEWS
| # Install 'depower' in R: |
| install.packages('depower', repos = c('https://bklamer.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://bitbucket.org/bklamer/depower
Last updated 17 days agofrom:fd12fc8d2d. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 09 2024 |
| R-4.5-win | OK | Dec 09 2024 |
| R-4.5-linux | OK | Dec 09 2024 |
| R-4.4-win | OK | Dec 09 2024 |
| R-4.4-mac | OK | Dec 09 2024 |
| R-4.3-win | OK | Dec 09 2024 |
| R-4.3-mac | OK | Dec 09 2024 |
Exports:glm_nbglmm_bnbglmm_poissonlrt_bnblrt_nbmle_bnb_altmle_bnb_nullmle_nb_altmle_nb_nullnll_bnb_altnll_bnb_nullnll_nb_altnll_nb_nullpowersim_bnbsim_log_lognormalsim_nbt_test_pairedt_test_welchwald_test_bnbwald_test_nb
Dependencies:BHbootcallrclicolorspacecrayondplyrfansifarvergenericsggplot2glmmTMBgluegtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixmgcvminqamultidplyrmunsellmvnfastnlmenloptrnumDerivpillarpkgconfigprocessxpsqsR6RApiSerializerbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRdpackreformulasrlangscalesstringfishtibbletidyselectTMButf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GLM for NB ratio of means | glm_nb |
| GLMM for BNB ratio of means | glmm_bnb |
| GLMM for Poisson ratio of means | glmm_poisson |
| Likelihood ratio test for BNB ratio of means | lrt_bnb |
| Likelihood ratio test for NB ratio of means | lrt_nb |
| MLE for BNB | mle_bnb mle_bnb_alt mle_bnb_null |
| MLE for NB | mle_nb mle_nb_alt mle_nb_null |
| Negative log-likelihood for BNB | nll_bnb nll_bnb_alt nll_bnb_null |
| Negative log-likelihood for NB | nll_nb nll_nb_alt nll_nb_null |
| Plot power objects | plot.depower |
| Simulated power | power |
| Simulate data from a BNB distribution | sim_bnb |
| Simulate data from a normal distribution | sim_log_lognormal |
| Simulate data from a NB distribution | sim_nb |
| Paired and one-sample t-Tests | t_test_paired |
| Welch's t-Test | t_test_welch |
| Wald test for BNB ratio of means | wald_test_bnb |
| Wald test for NB ratio of means | wald_test_nb |
