aSPU: Adaptive Sum of Powered Score Test
Version 1.47

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').

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AuthorIl-Youp Kwak and others (See Author(s) in each function manual)
Date of publication2017-05-21 07:38:23 UTC
MaintainerIl-Youp Kwak <ikwak@umn.edu>
LicenseGPL-3
Version1.47
URL https://github.com/ikwak2/aSPU
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("aSPU")

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...
aSPUpath2: 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...
aSPUsPath2: 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...
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

GATES2 Man page Source code
GEE Source code
GEEaSPU Man page Source code
GEEspu.score Source code
GatesSimes Man page Source code
Hyst Man page Source code
MTaSPUs Man page Source code
MTaSPUsB1e8 Source code
MTaSPUsSet Man page Source code
MTaSPUsSetPath Man page Source code
MTaSPUsSetScore Man page Source code
MTaSPUsmallB Source code
PermPvs Source code
PowerUniv Source code
SAMD11 Man page
Stat Source code
Sum Source code
SumSqU Source code
UminPd Source code
aSPU Man page Source code
aSPUboot Source code
aSPUboot2 Source code
aSPUd Man page Source code
aSPUpath Man page Source code
aSPUpath2 Man page Source code
aSPUperm Source code
aSPUperm2 Source code
aSPUpermC Source code
aSPUr Man page Source code
aSPUs Man page Source code
aSPUsD Man page Source code
aSPUsPath Man page Source code
aSPUsPath2 Man page Source code
aSPUsim1 Source code
aSPUsim2 Source code
aSPUw Man page Source code
aSPUwboot Source code
aSPUwboot2 Source code
aSPUwperm Source code
aSPUwsim Source code
chkRank.drop.cols Source code
estcov Man page Source code
exdat Man page
extractPCs Source code
getlogitp Man page Source code
kegg9 Man page
longForm Source code
minP Man page Source code
plotPmat Man page Source code
pruneSNP Man page Source code
simPathAR1Snp Man page Source code
someGs Man page

Files

inst
inst/doc
inst/doc/MTaSPUsSet.Rmd
inst/doc/aSPUstat.html
inst/doc/aSPUstat.R
inst/doc/MTaSPUsSet.html
inst/doc/MTaSPUsSet.R
inst/doc/aSPUstat.Rmd
NAMESPACE
data
data/someGs.rda
data/kegg9.rda
data/SAMD11.rda
data/exdat.rda
R
R/aSPUsD.R
R/aSPUboot2.R
R/aSPUwboot.R
R/aSPU.R
R/simPathAR1SNP.R
R/aSPUsPath2.r
R/MTaSPUsSetPath.R
R/aSPUd.R
R/getlogitp.R
R/aSPUperm2.R
R/MTaSPUsSetScore.R
R/aSPUwperm.R
R/GEEaSPU.R
R/aSPUperm.R
R/plotPmat.r
R/aSPUpath2.r
R/GatesSimes.R
R/aSPUpermC.R
R/Hyst.R
R/MTaSPUs.R
R/minP.R
R/aSPUw.R
R/estcov.R
R/aSPUboot.R
R/aSPUwsim.R
R/aSPUs.R
R/aSPUsim1.R
R/aSPUpath.r
R/aSPUsim2.R
R/util.R
R/MTaSPUsSet.R
R/GATES2.R
R/pruningSNP.R
R/aSPUr.R
R/aSPUsPath.r
vignettes
vignettes/MTaSPUsSet.Rmd
vignettes/aSPUstat.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/estcov.Rd
man/simPathAR1Snp.Rd
man/GEEaSPU.Rd
man/aSPUd.Rd
man/exdat.Rd
man/kegg9.Rd
man/aSPUr.Rd
man/MTaSPUsSetPath.Rd
man/GATES2.Rd
man/SAMD11.Rd
man/aSPU.Rd
man/minP.Rd
man/aSPUpath.Rd
man/aSPUsPath.Rd
man/MTaSPUsSetScore.Rd
man/aSPUw.Rd
man/MTaSPUs.Rd
man/Hyst.Rd
man/someGs.Rd
man/aSPUsPath2.Rd
man/pruneSNP.Rd
man/aSPUpath2.Rd
man/MTaSPUsSet.Rd
man/aSPUsD.Rd
man/plotPmat.Rd
man/aSPUs.Rd
man/GatesSimes.Rd
man/getlogitp.Rd
aSPU documentation built on May 23, 2017, 9:13 a.m.