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').
|Depends:||R (≥ 3.1.0), gee, MASS, mvtnorm, fields, matrixStats|
|Imports:||Rcpp (≥ 0.12.1)|
|Author:||Il-Youp Kwak and others (See Author(s) in each function manual)|
|Maintainer:||Il-Youp Kwak <ikwak at umn.edu>|
|CRAN checks:||aSPU results|
gene - multitrait aSPU with GWAS Summary Statistics
aSPU with GWAS Summary Statistics
|Windows binaries:||r-devel: aSPU_1.46.zip, r-release: aSPU_1.46.zip, r-oldrel: aSPU_1.46.zip|
|OS X Mavericks binaries:||r-release: aSPU_1.46.tgz, r-oldrel: aSPU_1.46.tgz|
|Old sources:||aSPU archive|
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