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: 1.47
Depends: R (≥ 3.1.0), gee, MASS, mvtnorm, fields, matrixStats
Suggests: knitr
Published: 2017-05-21
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak at umn.edu>
License: GPL-3
URL: https://github.com/ikwak2/aSPU
NeedsCompilation: no
Materials: README
CRAN checks: aSPU results

Downloads:

Reference manual: aSPU.pdf
Vignettes: gene - multitrait aSPU with GWAS Summary Statistics
aSPU with GWAS Summary Statistics
Package source: aSPU_1.47.tar.gz
Windows binaries: r-devel: aSPU_1.47.zip, r-release: aSPU_1.47.zip, r-oldrel: aSPU_1.47.zip
OS X El Capitan binaries: r-release: aSPU_1.47.tgz
OS X Mavericks binaries: r-oldrel: aSPU_1.47.tgz
Old sources: aSPU archive

Reverse dependencies:

Reverse depends: MiSPU

Linking:

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