Methylation Arrays ======================================================== author: Martin Morgan (mtmorgan@fhcrc.org), Fred Hutchinson Cancer Research, Center, Seattle, WA, USA. date: 24 August 2014 ```{r setup, include=FALSE} options(width=44) opts_chunk$set(cache=TRUE) ``` ```{r, include=FALSE} library(minfi) library(minfiData) ``` E.g., HumanMethylation450k ======================================================== - Interrogate fragmented whole-genome DNA for methylationat specific genomic locations Workflow 1. Experimental design: replicate groups - Wet-lab protocol - $\beta$: per-sample probe differential methylation - Quality assessment - Between-treatment differential methylation - Interpretation Illumina bead arrays ======================================================== ![Methylation workflow](figures/600px-Illuminamethylationworkflow.png) http://en.wikipedia.org/wiki/Illumina_Methylation_Assay Essential data ======================================================== Probe x Sample matrix of $\beta$ differential methylation values ```{r, echo=FALSE} library(minfi); library(minfiData) m <- getBeta(MsetEx)[1:6, 1:4] colnames(m) = sub(".*_", "", colnames(m)) m ``` 'Metadata' ======================================================== - Associated with features (`fData()`) and samples (`pData()`) - Important to coordinate with methylation values, e.g., subsetting - Solution: class to represent combined methylation and metadata *** ![ExpressionSet](figures/ExpressionSet.png) Example: ======================================================== ```{r} library(minfi) library(minfiData) MsetEx ``` Example: pData ======================================================== ```{r} head(pData(MsetEx), 3) ``` Example: subset ======================================================== ```{r} MsetEx[, pData(MsetEx)$status == "normal"] ``` 'S4' Classes ======================================================== - Similar to classes we have already seen - Different syntax for discovering methods, finding help ```{r, eval=FALSE} class(MsetEx) showMethods("pData", where=search()) showMethods(class=class(MSetEx), where=search()) class ? MethylSet method ? "getBeta,MethylSet" ``` Resources ======================================================== - `minfi` [landing page](http://bioconductor.org/packages/release/bioc/html/minfi.html) and vignette `browseVignettes("minfi")` - `Biobase` vignette "An Introduction to _Biobase_ and _ExpressionSet_", `browseVignettes("Biobase")` Acknowledgements ======================================================== Funding - US NIH / NHGRI 2U41HG004059; NSF 1247813 People - Seattle Bioconductor team: Sonali Arora, Marc Carlson, Nate Hayden, Valerie Obenchain, Hervé Pagès, Dan Tenenbaum - Vincent Carey, Robert Gentleman, Rafael Irizzary, Sean Davis, Kasper Hansen, Michael Lawrence, Levi Waldron