Il-Youp Kwak ikwak@umn.edu
R/aSPU is an R package for Genetic association testing methods such as aSPU, aSPUw, aSPUpath, aSPUs, aSPUsPath, GEEaSPU, MTaSPUs, GATES, GATE-Simes, HYST etc.
| Function Name | Data Type | Description |
|---|---|---|
| aSPU, aSPUw, aSPUr | Individual | Single trait; gene-based |
| aSPUs | Summary | Single trait; gene-based |
| aSPUpath | Individual | Single trait; pathway-based |
| aSPUsPath | Summary | Single trait; pathway-based |
| GEEaSPU | Individual | Multiple traits; single SNP based |
| MTaSPUs | Summary | Multiple traits; single SNP based |
| MTaSPUsSet | Summary | Multiple traits; gene-based |
| MTaSPUsSetPath | Summary | Multiple traits; pathway-based |
*Data type indicate the structure of data set. "Individual" for individual level data. "Summary" for summary statistics data (such as Z scores or p-values of each SNP)
Some tutorials for aSPUs, aSPUsPath and MTaSPUsSet are available.
- Mapping Snp to Gene
- Getting correlation estimate among SNPs from reference panel
- R and Perl codes to perform aSPUs and MTaSPUsSet
- Pathway data manipulation
- Speed comparison using R, awk and Perl
- Vignette for aSPUs and aSPUsPath
- Vignette for MTaSPUsSet
For 'aSPU'
Wei Pan, Junghi Kim, Yiwei Zhang, Xiaotong Shen and Peng Wei (2014)
A powerful and adaptive association test for rare variants,
Genetics, 197(4), 1081-95
For 'aSPUw'
Junghi Kim, Jeffrey R Wozniak, Bryon A Mueller, Xiaotong Shen and Wei Pan (2014)
Comparison of statistical tests for group differences in brain functional networks,
NeuroImage, 1;101:681-694
For 'aSPUr'
Peng Wei, Ying Cao, Yiwei Zhang, Zhiyuan Xu, Il-Youp Kwak, Eric Boerwinkle, Wei Pan (2016)
On Robust Association Testing for Quantitative Traits and Rare Variants, Submitted.
For 'aSPUpath'
Wei Pan, Il-Youp Kwak and Peng Wei (2015)
A Powerful and Pathway-Based Adaptive Test for Genetic Association With Common or Rare Variants,
The American Journal of Human Genetics 97, 86-98
For 'aSPUs' and 'aSPUsPath'
Il-Youp Kwak, Wei Pan (2015)
Adaptive Gene- and Pathway-Trait Association Testing with GWAS Summary Statistics,
Bioinformatics, doi: 10.1093/bioinformatics/btv719
For 'GEEaSPU'
Yiwei Zhang, Zhiyuan Xu, Xiaotong Shen, Wei Pan (2014)
Testing for association with multiple traits in generalized estimation equations, with application to neuroimaging data,
Neuroimage. 96:309-25
For 'MTaSPUs'
Junghi Kim, Yun Bai and Wei Pan (2015)
An Adaptive Association Test for Multiple Phenotypes with GWAS Summary Statistics,
Genetic Epidemiology, 8:651-663
For 'MTaSPUsSet' and 'MTaSPUsSetPath'
Il-Youp Kwak, Wei Pan (2016)
Gene- and pathway-based association tests for multiple traits with GWAS summary statistics
For 'GATES'
Miao-Xin Li, Hong-Sheng Gui, Johnny S.H. Kwan and Pak C. Sham (2011)
GATES: A Rapid and Powerful Gene-Based Association Test Using Extended Simes Procedure,
The American Journal of Human Genetics 88, 283-293
For 'GATES-Simes'
Hongsheng Gui, Miaoxin Li, Pak C Sham and Stacey S Cherny (2011)
Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn's Disease
BMC Research Notes, 4:386
For 'HYST'
Miao-Xin Li, Johnny S.H. Kwan and Pak C. Sham (2012)
HYST: A Hybrid Set-Based Test for Genome-wide Association Studies, with Application to Protein-Protein Interaction-Based Association Analysis
The American Journal of Human Genetics, 91, 478-488.
From CRAN :
install.packages("aSPU")Or, with devtools:
library(devtools)
install_github("ikwak2/aSPU")