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aSPU
Adaptive Sum of Powered Score Test
View on CRAN: Click
here
Download and install aSPU package within the R console
Install from CRAN:
install.packages("aSPU")
Install from Github:
library("remotes")
install_github("cran/aSPU") Install by package version:
library("remotes")
install_version("aSPU", "1.50") Attach the package and use:
library("aSPU")
Maintained by
Il-Youp Kwak
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-05-28
Latest Update: 2021-06-28
Description:
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').
How to cite:
Il-Youp Kwak (2015). aSPU: Adaptive Sum of Powered Score Test. R package version 1.50, https://cran.r-project.org/web/packages/aSPU. Accessed 22 Dec. 2024.
Previous versions and publish date:
1.33 (2015-05-28 00:47), 1.35 (2015-06-04 07:41), 1.36 (2015-07-28 08:03), 1.37 (2015-08-03 19:34), 1.38 (2015-10-26 23:00), 1.39 (2015-12-22 08:01), 1.40 (2016-02-18 18:46), 1.41 (2016-03-22 00:23), 1.42 (2016-05-03 02:08), 1.43 (2016-09-15 12:20), 1.44 (2016-09-22 16:50), 1.45 (2016-10-12 00:03), 1.46 (2016-11-09 00:37), 1.47 (2017-05-21 09:38), 1.48 (2017-06-25 00:22), 1.49 (2020-05-13 09:50)
Other packages that cited aSPU R package
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Other R packages that aSPU depends,
imports, suggests or enhances
Complete documentation for aSPU
Functions, R codes and Examples using
the aSPU R package
Some associated functions: GATES2 . GEEaSPU . GatesSimes . Hyst . MTaSPUs . MTaSPUsSet . MTaSPUsSetPath . MTaSPUsSetScore . SAMD11 . aSPU . aSPUd . aSPUpath . aSPUpath2 . aSPUr . aSPUs . aSPUsD . aSPUsPath . aSPUsPath2 . aSPUw . estcov . exdat . getlogitp . kegg9 . minP . plotPmat . pruneSNP . simPathAR1Snp . someGs .
Some associated R codes: GATES2.R . GEEaSPU.R . GatesSimes.R . Hyst.R . MTaSPUs.R . MTaSPUsSet.R . MTaSPUsSetPath.R . MTaSPUsSetScore.R . aSPU.R . aSPUboot.R . aSPUboot2.R . aSPUd.R . aSPUperm.R . aSPUperm2.R . aSPUpermC.R . aSPUr.R . aSPUs.R . aSPUsD.R . aSPUsim1.R . aSPUsim2.R . aSPUw.R . aSPUwboot.R . aSPUwperm.R . aSPUwsim.R . estcov.R . getlogitp.R . minP.R . pruningSNP.R . simPathAR1SNP.R . util.R . Full aSPU package functions and examples
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