Uses for GBJ | Worked Example - Individual Level Genotype Data | Worked Example - Summary Statistics | Some advice for special cases
Package: GBJ 0.5.4
GBJ: Generalized Berk-Jones Test for Set-Based Inference in Genetic Association Studies
Offers the Generalized Berk-Jones (GBJ) test for set-based inference in genetic association studies. The GBJ is designed as an alternative to tests such as Berk-Jones (BJ), Higher Criticism (HC), Generalized Higher Criticism (GHC), Minimum p-value (minP), and Sequence Kernel Association Test (SKAT). All of these other methods (except for SKAT) are also implemented in this package, and we additionally provide an omnibus test (OMNI) which integrates information from each of the tests. The GBJ has been shown to outperform other tests in genetic association studies when signals are correlated and moderately sparse. Please see the vignette for a quickstart guide or Sun and Lin (2017) <arxiv:1710.02469> for more details.
Authors:
GBJ_0.5.4.tar.gz
GBJ_0.5.4.zip(r-4.7-x86_64)GBJ_0.5.4.zip(r-4.6-x86_64)GBJ_0.5.4.zip(r-4.5-x86_64)
GBJ_0.5.4.tgz(r-4.6-x86_64)GBJ_0.5.4.tgz(r-4.6-arm64)GBJ_0.5.4.tgz(r-4.5-x86_64)GBJ_0.5.4.tgz(r-4.5-arm64)
GBJ_0.5.4.tar.gz(r-4.7-arm64)GBJ_0.5.4.tar.gz(r-4.7-x86_64)GBJ_0.5.4.tar.gz(r-4.6-arm64)GBJ_0.5.4.tar.gz(r-4.6-x86_64)
GBJ_0.5.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GBJ/json (API)
| # Install 'GBJ' in R: |
| install.packages('GBJ', repos = c('https://ryansunwork.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:bc40c99b67. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 196 | ||
| linux-devel-x86_64 | OK | 237 | ||
| source / vignettes | OK | 214 | ||
| linux-release-arm64 | OK | 188 | ||
| linux-release-x86_64 | OK | 205 | ||
| macos-release-arm64 | OK | 124 | ||
| macos-release-x86_64 | OK | 311 | ||
| macos-oldrel-arm64 | OK | 106 | ||
| macos-oldrel-x86_64 | OK | 285 | ||
| windows-devel | OK | 129 | ||
| windows-release | OK | 140 | ||
| windows-oldrel | OK | 139 | ||
| wasm-release | OK | 120 |
Exports:BJcalc_score_statscalc_var_nonzero_muebb_loglikestimate_ss_corGBJGBJ_objectiveGBJ_pvalueGHCGHC_objectiveHCherm_poly_diff_tminPOMNI_individualOMNI_ssparse_inputqnorm_muscore_stats_onlysurv
Dependencies:BHlatticeMatrixmvtnormRcppRcppEigenRSpectraSKATSPAtest
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BJ.R | BJ |
| calc_score_stats.R | calc_score_stats |
| estimate_ss_cor.R | estimate_ss_cor |
| Genotypes at FGFR2 SNPs for subjects from 'GBR' population in the 1000 Genomes Project. | FGFR2 |
| GBJ.R | GBJ |
| GBJ_pvalue.R | GBJ_pvalue |
| Simulated Principal Components for 'GBR' population in the 1000 Genomes Project. | gbr_pcs |
| GHC.R | GHC |
| HC.R | HC |
| minP.R | minP |
| omni_individual.R | OMNI_individual |
| omni_ss.R | OMNI_ss |
| score_stats_only.R | score_stats_only |
| surv.R | surv |
