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---
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.
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"