Last updated: 2020-05-15

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Knit directory: methyl-geneset-testing/

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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. Follow the links below to explore the different parts of the project.

Analysis

Explore EPIC array bias
- EPIC array bias - Explore the various array biases that affect gene set testing.
Explore 450k array bias
- 450k array bias - Explore the various array biases that affect gene set testing.
Blood cell RNAseq “truth” set
- RNAseq analysis - Analyse an RNAseq sorted blood cell dataset and identify the top ranked gene sets for each cell type comparison.
Compare methods
- Compare methods - Analyse an EPIC array sorted blood cell dataset using various gene set testing methods. Compare the results of the different methods.
Compare run-time of methods
- Compare run-time - Analyse an EPIC array sorted blood cell dataset using various gene set testing methods. Compare the run-time of the different methods.
Compare false discovery rate of different methods
- Compare false discovery rate - Analyse the normal samples from a 450k array KIRC TCGA dataset using various genset testing methods to estimate their false discovery rate control.
Gene set testing of regions
- Region analysis - Evalulate the use of gometh for geneset testing of differentially methylated regions from region finding software.

Licenses

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

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Gene set testing for methylation arrays

Analysis

Licenses

Citations