index.Rmd

---
title: "Home"
site: workflowr::wflow_site
output:
  workflowr::wflow_html:
    toc: false
---

# Gene set testing for methylation arrays

This site contains the development and evaluation of various methylation array 
gene set testing methods available in the Bioconductor [missMethyl package](https://bioconductor.org/packages/release/bioc/html/missMethyl.html). 
Follow the links below to explore the 
different parts of the project. 


Analysis
--------
1. [Explore EPIC array bias](exploreArrayBiasEPIC.html)
    * Explore the various array biases on the EPIC array that affect gene set testing.
      
2. [Explore 450k array bias](exploreArrayBias450.html)
    * Explore the various array biases on the 450k array that affect gene set testing.

3. [Generate a blood cell RNAseq "truth" set](expressionGenesets.html)
    * Analyse an RNAseq sorted blood cell dataset and identify the top ranked 
      gene sets for each cell type comparison.
      
4. [Compare FDR of different methods](fdrAnalysis.html)
    * Analyse the normal samples from a 450k array KIRC TCGA dataset using 
      various genset testing methods to estimate their false discovery rate control.
      
5. [Compare performance of different methods](exploreData.html)
    * Analyse an EPIC array sorted blood cell dataset using various gene set 
      testing methods. Compare how well the different methods perform using several 
      metrics.

6. [Compare run-time of different methods](runTimeComparison.html)
    * Analyse an EPIC array sorted blood cell dataset using various gene set 
      testing methods. Compare the run-time of the different methods.

7. [Effect of gene set size parameters on methylGSA](methylGSAParamSweep.html)
    * Analyse an EPIC array sorted blood cell dataset using various gene set 
      testing methods. Compare the run-time of the different methods.
      
8. [Evaluate GOregion](regionAnalysis.html)
    * Evalulate GOregion, our extension of gometh for geneset testing of 
      differentially methylated regions (DMRs) identified by DMR finding software.

9. [Restricting Sig. CpGs in GOmeth by genomic region](gomethByFeature.html)
    * Evalulate the impact of on gene set testing using GOmeth of restricting 
      significant CpGs based on genomic feature using the EPIC sorted blood cell 
      dataset.
      
```{r}
library(glue)
prefix <- "https://atlassian.petermac.org.au/bitbucket/pages/OS/methyl-geneset-testing/master/browse/output/"
fig <- "Fig-1A.pdf"
link <- glue("{prefix}{fig}")
```

[Figure 1A](`r cat(link)`)

Licenses
--------

The code in this analysis is covered by the [MIT license][mit] and the written
content on this website is covered by a [Creative Commons CC-BY][cc] license.


Citations
---------

[mit]: https://choosealicense.com/licenses/mit/ "MIT License"
[cc]: https://creativecommons.org/licenses/by/4.0/ "CC-BY License"