R: Adaptive Sum of Powered Score Test

# Adaptive Sum of Powered Score Test

## Documentation for package ‘aSPU’ version 1.50

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

aSPU | Sum of Powered Score (SPU) tests and adaptive SPU (aSPU) test for single trait - SNP set association.
aSPUd | Adaptive Sum of powered score (SPU) tests (SPU and aSPU) based on asymptotic distribution.
aSPUpath | Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for single trait - pathway association.
aSPUpath2 | Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for single trait - pathway association. (vector version, fast when n is large)
aSPUr | Robust Sum of powered score (SPU) tests and aSPU test for a quantitative trait
aSPUs | Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs) test for single trait - SNP set association with GWAS summary statistics.
aSPUsD | Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs) test for single trait - SNP set association with GWAS summary statistics (distribution based).
aSPUsPath | Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics.
aSPUsPath2 | Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics. (vector version, fast when n is large)
aSPUw | Inverse variance weighted Sum of Powered Score tests (SPUw) and adaptive SPUw (aSPUw) test for single trait - SNP set association.
estcov | estcov
exdat | An example data set
GATES2 | Gene-based Association Test that uses an extended Simes procedure (GATES) for single trait - SNP set association
GatesSimes | GATES-Simes test for single trait - pathway association.
GEEaSPU | The SPU and aSPU tests for multiple traits - single SNP association in generalized estimating equations.
getlogitp | Get the p-values of the multiple SNPs based on the Wald test in a logistic regresion model.
Hyst | HYST (Hybrid Set-based Test) for single trait - pathway association
kegg9 | A subset of coronary artery disease (CAD) data
minP | minP test.
MTaSPUs | The SPU and aSPU tests for multiple traits - single SNP association with GWAS summary statistics.
MTaSPUsSet | gene-Multitrait Sum of Powered Score (MTSPUsSet) tests and adaptive MTSPUsSet (MTaSPUsSet) test for multi trait - SNP set association with GWAS summary statistics.
MTaSPUsSetPath | Multitraits - Pathway based Sum of Powered Score tests (MTSPUsSetPath) and adaptive MTSPUsSetpath (MTaSPUsSetPath) test for multi trait - pathway association with GWAS summary statistics.
MTaSPUsSetScore | gene-Multitrait Sum of Powered Score (MTSPUsSetScore) tests and adaptive MTSPUsSet (MTaSPUsSet) test for multi trait - SNP set association with GWAS summary statistics. (Score version added)
plotPmat | Image plot of P-value matrix.
pruneSNP | Prune SNPs (related to aSPUs, aSPUsPath, MTaSPUsSet)
SAMD11 | An example data for MTaSPUsSet test
simPathAR1Snp | Simulating a pathway with multiple SNPs.
someGs | An example data for MTaSPUsSet test