ikwak2 / aSPU_tutorials

Some tutorial documents for aSPUs, aSPUsPath, MTaSPUsSet and MTaSPUsSetPath.

Some tutorials for aSPU

Il-Youp Kwak [e-mail]

This tutorial illustrate how one can perform gene-based analysis with simple examples.

Contents

• Mapping Snp to Gene
  • Assume you have rs-ids, and you want to map rs-ids to gene for gene based analysis. This page illustrate one way to do this.
• Getting correlation estimate among SNPs from reference panel
  • This page illustrate how one can get correlation estimate among SNPs from the reference panel.
• R and Perl codes to perform aSPUs and MTaSPUsSet
  • Assume we have multi-trait summary statistics data for mapped SNPs from Mapping Snp to Gene, this page illustrate how to perform aSPUs or MTaSPUsSet test using Summary Statistics data.
• Speed comparison using R, awk and Perl
  • I used awk in some tutorials. I do some speed comparison here.
• Pathway data manipulation
  • Where to get pathways(or gene sets) and how to manipulate.
• Vignette for aSPUs and aSPUsPath
  • Adaptive Gene- and Pathway- Trait Association testing with GWAS Summary Statistics (aSPUs() and aSPUsPath())
• Vignette for MTaSPUsSet
  • Adaptive Gene - Multitrait Association testing with GWAS Summary Statistics (MTaSPUsSet() )

Part of the data here downloaded from GIANT consortium data files website. Data is originally from Randall JC, Winkler TW, Kutalik Z, Berndt SI, Jackson AU, Monda KL, Kilpeläinen TO, Esko T, Mägi R, Li S, et al. (2013). Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits. PLoS Genet 9: e1003500.