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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').

Version: 1.50
Depends: R (≥ 3.6.0), gee, MASS, mvtnorm, fields, matrixStats
Suggests: rmarkdown, markdown, knitr
Published: 2021-06-28
DOI: 10.32614/CRAN.package.aSPU
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

Documentation:

Reference manual: aSPU.pdf
Vignettes: aSPU with GWAS Summary Statistics
gene - multitrait aSPU with GWAS Summary Statistics

Downloads:

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 dependencies:

Reverse depends: MiSPU

Linking:

Please use the canonical form https://CRAN.R-project.org/package=aSPU to link to this page.

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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