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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').
| Version: | 1.50 |
| Depends: | R (≥ 3.6.0), gee, MASS, mvtnorm, fields, matrixStats |
| Suggests: | rmarkdown, markdown, knitr |
| Published: | 2021-06-28 |
| Author: | Il-Youp Kwak and others (See Author(s) in each function manual) |
| Maintainer: | Il-Youp Kwak <ikwak2 at cau.ac.kr> |
| License: | GPL-3 |
| URL: | https://github.com/ikwak2/aSPU |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | aSPU results |
| Reference manual: | aSPU.pdf |
| Vignettes: |
aSPU with GWAS Summary Statistics gene - multitrait aSPU with GWAS Summary Statistics |
| Package source: | aSPU_1.50.tar.gz |
| Windows binaries: | r-devel: aSPU_1.50.zip, r-release: aSPU_1.50.zip, r-oldrel: aSPU_1.50.zip |
| macOS binaries: | r-release (arm64): aSPU_1.50.tgz, r-oldrel (arm64): aSPU_1.50.tgz, r-release (x86_64): aSPU_1.50.tgz, r-oldrel (x86_64): aSPU_1.50.tgz |
| Old sources: | aSPU archive |
| Reverse depends: | MiSPU |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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