R Methy VIII: ChAMP2

The final steps for performing a full ChAMP pipeline analysis is

• Perform a Geneset Enrichment Analysis using champ.GSEA()
• Perform Methylation Interaction Hotspot analysis using champ.EpiMod(). This one takes long time to run, so you might want to keep it for last.
• Perform Copy Number Variation analysis using champ.CNA()

Questions

17. How many significant gene lists did you find? Which genelist has the largest odds ratio (OR)? Why does not this genelist have the smallest p-value?
18. Hand in epimod-plot for the most significant module
19. Which tumor samples has the most copy number changes?

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