Last updated: 2020-03-02

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Knit directory: methyl-geneset-testing/

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Rmd d7cd66e Jovana Maksimovic 2020-03-02 Initial Commit
Rmd 1840409 Jovana Maksimovic 2020-03-02 Start workflowr project.

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.
  • 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 false discovery rate of different methods
    • Compare false discovery rate - Analyse the normal samples from a 450k array rheumatoid arthritis dataset using various genset testing methods to estimate the 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.

Citations