On R/DrImpute
- Vignette for DrImpute
- This vignette illustrates the use of DrImpute software in single cell RNA sequencing data analysis.
On R/aSPU
- 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 it.
- 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 did some speed comparisons.
- 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() )
On R/funqtl
Vignette for funqtl
This vignette illustrates the use of the funqtl package for QTL mapping with function-valued traits (e.g., growth measured over time).
Vignette for fun2mult
This vignette illustrates the use of the funqtl package for QTL mapping with function-valued traits using functional principal component analysis and multi-trait mapping.
Part of the data here downloaded from GIANT consortium data files website. Data is 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.
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