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'), (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').

Version: 1.39
Depends: R (≥ 3.1.0), gee, MASS, mvtnorm, matrixStats
Imports: Rcpp (≥ 0.12.1)
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr
Published: 2015-12-22
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: yes
Materials: README
CRAN checks: aSPU results

Downloads:

Reference manual: aSPU.pdf
Vignettes: aSPU with GWAS Summary Statistics
Package source: aSPU_1.39.tar.gz
Windows binaries: r-devel: aSPU_1.39.zip, r-release: aSPU_1.39.zip, r-oldrel: aSPU_1.39.zip
OS X Snow Leopard binaries: r-release: aSPU_1.39.tgz, r-oldrel: not available
OS X Mavericks binaries: r-release: aSPU_1.39.tgz
Old sources: aSPU archive