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').

Install the latest version of this package by entering the following in R:
install.packages("aSPU")
AuthorIl-Youp Kwak and others (See Author(s) in each function manual)
Date of publication2016-11-09 00:37:10
MaintainerIl-Youp Kwak <ikwak@umn.edu>
LicenseGPL-3
Version1.46
https://github.com/ikwak2/aSPU

View on CRAN

Man pages

aSPU: Sum of Powered Score (SPU) tests and adaptive SPU (aSPU) test...

aSPUd: Adaptive Sum of powered score (SPU) tests (SPU and aSPU)...

aSPUpath: Pathway based Sum of Powered Score tests (SPUpath) and...

aSPUr: Robust Sum of powered score (SPU) tests and aSPU test for a...

aSPUs: Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs)...

aSPUsD: Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs)...

aSPUsPath: Pathway based Sum of Powered Score tests (SPUsPath) and...

aSPUw: Inverse variance weighted Sum of Powered Score tests (SPUw)...

estcov: estcov

exdat: An example data set

GATES2: Gene-based Association Test that uses an extended Simes...

GatesSimes: GATES-Simes test for single trait - pathway association.

GEEaSPU: The SPU and aSPU tests for multiple traits - single SNP...

getlogitp: Get the p-values of the multiple SNPs based on the Wald test...

Hyst: HYST (Hybrid Set-based Test) for single trait - pathway...

kegg9: A subset of coronary artery disease (CAD) data

minP: minP test.

MTaSPUs: The SPU and aSPU tests for multiple traits - single SNP...

MTaSPUsSet: gene-Multitrait Sum of Powered Score (MTSPUsSet) tests and...

MTaSPUsSetC: gene-Multitrait Sum of Powered Score (MTSPUsSet) tests and...

MTaSPUsSetPath: Multitraits - Pathway based Sum of Powered Score tests...

MTaSPUsSetScore: gene-Multitrait Sum of Powered Score (MTSPUsSetScore) tests...

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

Functions

aSPU Man page
aSPUd Man page
aSPUpath Man page
aSPUr Man page
aSPUs Man page
aSPUsD Man page
aSPUsPath Man page
aSPUw Man page
estcov Man page
exdat Man page
GATES2 Man page
GatesSimes Man page
GEEaSPU Man page
getlogitp Man page
Hyst Man page
kegg9 Man page
minP Man page
MTaSPUs Man page
MTaSPUsSet Man page
MTaSPUsSetC Man page
MTaSPUsSetPath Man page
MTaSPUsSetScore Man page
plotPmat Man page
pruneSNP Man page
SAMD11 Man page
simPathAR1Snp Man page
someGs Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.