Package: aSPU 1.50

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').

Authors:Il-Youp Kwak and others

aSPU_1.50.tar.gz
aSPU_1.50.zip(r-4.7)aSPU_1.50.zip(r-4.6)aSPU_1.50.zip(r-4.5)
aSPU_1.50.tgz(r-4.6-any)aSPU_1.50.tgz(r-4.5-any)
aSPU_1.50.tar.gz(r-4.7-any)aSPU_1.50.tar.gz(r-4.6-any)
aSPU_1.50.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
aSPU/json (API)

# Install 'aSPU' in R:
install.packages('aSPU', repos = c('https://ikwak2.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ikwak2/aspu/issues

Datasets:
  • exdat - An example data set
  • kegg9 - A subset of coronary artery disease (CAD) data
  • SAMD11 - An example data for MTaSPUsSet test
  • someGs - An example data for MTaSPUsSet test

On CRAN:

Conda:

6.74 score 12 stars 46 scripts 422 downloads 11 mentions 24 exports 11 dependencies

Last updated from:6d6fab0296. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK128
source / vignettesOK227
linux-release-x86_64OK142
macos-release-arm64OK192
macos-oldrel-arm64OK149
windows-develOK89
windows-releaseOK83
windows-oldrelOK97
wasm-releaseOK141

Exports:aSPUaSPUdaSPUpathaSPUpath2aSPUraSPUsaSPUsDaSPUsPathaSPUsPath2aSPUwestcovGATES2GatesSimesGEEaSPUgetlogitpHystminPMTaSPUsMTaSPUsSetMTaSPUsSetPathMTaSPUsSetScoreplotPmatpruneSNPsimPathAR1Snp

Dependencies:dotCall64fieldsgeemapsMASSmatrixStatsmvtnormRColorBrewerRcppspamviridisLite

Adaptive Gene- and Pathway- Trait Association testing with GWAS Summary Statistics (aSPUs() and aSPUsPath())
Data | Use of aSPUs function | Use of aSPUsPath function
Rendered fromaSPUstat.Rmdusingknitr::rmarkdown

Last update: 2021-06-28
Started: 2015-07-24

Adaptive Gene - Multitrait Association testing with GWAS Summary Statistics (MTaSPUsSet() )
Data preparation | Data analysis | Data Visualization of some detected genes
Rendered fromMTaSPUsSet.Rmdusingknitr::rmarkdown

Last update: 2021-06-28
Started: 2016-03-24

Readme and manuals

Help Manual

Help pageTopics
Sum of Powered Score (SPU) tests and adaptive SPU (aSPU) test for single trait - SNP set association.aSPU
Adaptive Sum of powered score (SPU) tests (SPU and aSPU) based on asymptotic distribution.aSPUd
Pathway based Sum of Powered Score tests (SPUpath) and adaptive SPUpath (aSPUpath) test for single trait - pathway association.aSPUpath
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)aSPUpath2
Robust Sum of powered score (SPU) tests and aSPU test for a quantitative traitaSPUr
Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs) test for single trait - SNP set association with GWAS summary statistics.aSPUs
Sum of Powered Score (SPUs) tests and adaptive SPU (aSPUs) test for single trait - SNP set association with GWAS summary statistics (distribution based).aSPUsD
Pathway based Sum of Powered Score tests (SPUsPath) and adaptive SPUpath (aSPUsPath) test for single trait - pathway association with GWAS summary statistics.aSPUsPath
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)aSPUsPath2
Inverse variance weighted Sum of Powered Score tests (SPUw) and adaptive SPUw (aSPUw) test for single trait - SNP set association.aSPUw
estcovestcov
An example data setexdat
Gene-based Association Test that uses an extended Simes procedure (GATES) for single trait - SNP set associationGATES2
GATES-Simes test for single trait - pathway association.GatesSimes
The SPU and aSPU tests for multiple traits - single SNP association in generalized estimating equations.GEEaSPU
Get the p-values of the multiple SNPs based on the Wald test in a logistic regresion model.getlogitp
HYST (Hybrid Set-based Test) for single trait - pathway associationHyst
A subset of coronary artery disease (CAD) datakegg9
minP test.minP
The SPU and aSPU tests for multiple traits - single SNP association with GWAS summary statistics.MTaSPUs
gene-Multitrait Sum of Powered Score (MTSPUsSet) tests and adaptive MTSPUsSet (MTaSPUsSet) test for multi trait - SNP set association with GWAS summary statistics.MTaSPUsSet
Multitraits - Pathway based Sum of Powered Score tests (MTSPUsSetPath) and adaptive MTSPUsSetpath (MTaSPUsSetPath) test for multi trait - pathway association with GWAS summary statistics.MTaSPUsSetPath
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)MTaSPUsSetScore
Image plot of P-value matrix.plotPmat
Prune SNPs (related to aSPUs, aSPUsPath, MTaSPUsSet)pruneSNP
An example data for MTaSPUsSet testSAMD11
Simulating a pathway with multiple SNPs.simPathAR1Snp
An example data for MTaSPUsSet testsomeGs