Adaptive Sum of Powered Score Test


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Documentation for package ‘aSPU’ version 1.49

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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