Package: aSPU 1.50
aSPU: Adaptive Sum of Powered Score Test
R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single nucleotide polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended 'Simes' procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits- single 'SNP' association with summary statistics ('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics('MTaSPUsSetPath').
Authors:
aSPU_1.50.tar.gz
aSPU_1.50.zip(r-4.5)aSPU_1.50.zip(r-4.4)aSPU_1.50.zip(r-4.3)
aSPU_1.50.tgz(r-4.4-any)aSPU_1.50.tgz(r-4.3-any)
aSPU_1.50.tar.gz(r-4.5-noble)aSPU_1.50.tar.gz(r-4.4-noble)
aSPU_1.50.tgz(r-4.4-emscripten)aSPU_1.50.tgz(r-4.3-emscripten)
aSPU.pdf |aSPU.html✨
aSPU/json (API)
| # Install 'aSPU' in R: |
| install.packages('aSPU', repos = c('https://ikwak2.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ikwak2/aspu/issues
Last updated 3 years agofrom:6d6fab0296. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 04 2024 |
| R-4.5-win | OK | Sep 04 2024 |
| R-4.5-linux | OK | Sep 04 2024 |
| R-4.4-win | OK | Sep 04 2024 |
| R-4.4-mac | OK | Sep 04 2024 |
| R-4.3-win | OK | Sep 04 2024 |
| R-4.3-mac | OK | Sep 04 2024 |
Exports:aSPUaSPUdaSPUpathaSPUpath2aSPUraSPUsaSPUsDaSPUsPathaSPUsPath2aSPUwestcovGATES2GatesSimesGEEaSPUgetlogitpHystminPMTaSPUsMTaSPUsSetMTaSPUsSetPathMTaSPUsSetScoreplotPmatpruneSNPsimPathAR1Snp
Dependencies:dotCall64fieldsgeemapsMASSmatrixStatsmvtnormRcppspamviridisLite
Adaptive Gene- and Pathway- Trait Association testing with GWAS Summary Statistics (aSPUs() and aSPUsPath())
Rendered fromaSPUstat.Rmdusingknitr::rmarkdownon Sep 04 2024.Last update: 2021-06-28
Started: 2015-07-24
Adaptive Gene - Multitrait Association testing with GWAS Summary Statistics (MTaSPUsSet() )
Rendered fromMTaSPUsSet.Rmdusingknitr::rmarkdownon Sep 04 2024.Last update: 2021-06-28
Started: 2016-03-24
