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.html , aSPU.pdf
Vignettes:	aSPU with GWAS Summary Statistics (source, R code) gene - multitrait aSPU with GWAS Summary Statistics (source, R code)

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:

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