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').

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

Files in this package

aSPU
aSPU/inst
aSPU/inst/doc
aSPU/inst/doc/MTaSPUsSet.Rmd
aSPU/inst/doc/aSPUstat.html
aSPU/inst/doc/aSPUstat.R
aSPU/inst/doc/MTaSPUsSet.html
aSPU/inst/doc/MTaSPUsSet.R
aSPU/inst/doc/aSPUstat.Rmd
aSPU/src
aSPU/src/Makevars
aSPU/src/util.c
aSPU/src/R_get_pv.c
aSPU/src/R_get_pvs2.c
aSPU/src/R_get_pvs.c
aSPU/src/aSPU.cpp
aSPU/src/util.h
aSPU/src/Makevars.win
aSPU/src/RcppExports.cpp
aSPU/NAMESPACE
aSPU/data
aSPU/data/someGs.rda
aSPU/data/kegg9.rda
aSPU/data/SAMD11.rda
aSPU/data/exdat.rda
aSPU/R
aSPU/R/aSPUsD.R aSPU/R/aSPUboot2.R aSPU/R/aSPUwboot.R aSPU/R/aSPU.R aSPU/R/aSPUsimC2.R aSPU/R/simPathAR1SNP.R aSPU/R/aSPUpermC2.R aSPU/R/MTaSPUsSetPath.R aSPU/R/aSPUd.R aSPU/R/getlogitp.R aSPU/R/aSPUperm2.R aSPU/R/MTaSPUsSetScore.R aSPU/R/aSPUwperm.R aSPU/R/GEEaSPU.R aSPU/R/aSPUperm.R
aSPU/R/plotPmat.r
aSPU/R/GatesSimes.R aSPU/R/aSPUpermC.R aSPU/R/Hyst.R aSPU/R/RcppExports.R aSPU/R/MTaSPUs.R aSPU/R/minP.R aSPU/R/aSPUw.R aSPU/R/estcov.R aSPU/R/MTaSPUsSetC.R aSPU/R/aSPUboot.R aSPU/R/aSPUwsim.R aSPU/R/aSPUs.R aSPU/R/aSPUsim1.R
aSPU/R/aSPUpath.r
aSPU/R/aSPUsim2.R aSPU/R/util.R aSPU/R/aSPUwpermC.R aSPU/R/MTaSPUsSet.R aSPU/R/GATES2.R aSPU/R/pruningSNP.R aSPU/R/aSPUr.R
aSPU/R/aSPUsPath.r
aSPU/vignettes
aSPU/vignettes/MTaSPUsSet.Rmd
aSPU/vignettes/aSPUstat.Rmd
aSPU/README.md
aSPU/MD5
aSPU/build
aSPU/build/vignette.rds
aSPU/DESCRIPTION
aSPU/man
aSPU/man/estcov.Rd aSPU/man/simPathAR1Snp.Rd aSPU/man/GEEaSPU.Rd aSPU/man/aSPUd.Rd aSPU/man/exdat.Rd aSPU/man/kegg9.Rd aSPU/man/aSPUr.Rd aSPU/man/MTaSPUsSetPath.Rd aSPU/man/GATES2.Rd aSPU/man/SAMD11.Rd aSPU/man/aSPU.Rd aSPU/man/minP.Rd aSPU/man/aSPUpath.Rd aSPU/man/aSPUsPath.Rd aSPU/man/MTaSPUsSetScore.Rd aSPU/man/aSPUw.Rd aSPU/man/MTaSPUs.Rd aSPU/man/Hyst.Rd aSPU/man/someGs.Rd aSPU/man/pruneSNP.Rd aSPU/man/MTaSPUsSet.Rd aSPU/man/aSPUsD.Rd aSPU/man/plotPmat.Rd aSPU/man/aSPUs.Rd aSPU/man/MTaSPUsSetC.Rd aSPU/man/GatesSimes.Rd aSPU/man/getlogitp.Rd

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