Last updated: 2020-06-01

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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

  1. Explore EPIC array bias
    • Explore the various array biases on the EPIC array that affect gene set testing.
  2. Explore 450k array bias
    • Explore the various array biases on the 450k array that affect gene set testing.
  3. Generate a blood cell RNAseq “truth” set
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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 and the written content on this website is covered by a Creative Commons CC-BY license.

Citations