aSPU: Adaptive Sum of Powered Score Test

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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').

Author
Il-Youp Kwak and others (See Author(s) in each function manual)
Date of publication
2016-11-09 00:37:10
Maintainer
Il-Youp Kwak <ikwak@umn.edu>
License
GPL-3
Version
1.46
URLs

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