%\VignetteIndexEntry{Working with Illumina 450k Arrays using methylumi}
%\VignetteEngine{knitr::knitr}
%\VignetteDepends{FDb.InfiniumMethylation.hg19}
%\VignetteDepends{TCGAMethylation450k}
%\VignetteDepends{Homo.sapiens}
%\VignetteDepends{TxDb.Hsapiens.UCSC.hg19.knownGene}
%\VignetteDepends{minfi}
%\VignetteDepends{lumi}
%\VignettePackage{methylumi}
\documentclass[12pt]{article}
\usepackage{amsmath}
\usepackage{fullpage}
\usepackage{hyperref}
\usepackage[authoryear,round]{natbib}
\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Robject}[1]{{\texttt{#1}}}
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<<include=FALSE>>=
library(knitr)
opts_chunk$set(tidy=FALSE,cache=TRUE,size='scriptsize')
@

\begin{document}
\setkeys{Gin}{width=0.8\textwidth} 
\author{Tim Triche, Jr. \& Sean Davis}
\title{Working with Illumina 450k Methylation Arrays}
\maketitle

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\tableofcontents
\clearpage
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\section{Creating a MethyLumiSet object from IDATs}

This also happens to be the first step in the TCGA processing pipeline.
The complete pipeline is available on GitHub as the EGC.tools project.
Ten samples from the TCGA breast cancer (BRCA) project are included in 
the TCGAMethylation450k package, which should be installed for this step.

<<setup,eval=TRUE,hide=TRUE,echo=FALSE>>=
options('width'=50)
@ 

<<loadLibraries, eval=TRUE>>=
suppressPackageStartupMessages(require('methylumi'))
suppressPackageStartupMessages(require('TCGAMethylation450k'))
suppressPackageStartupMessages(require('FDb.InfiniumMethylation.hg19'))
@ 

<<loadData, eval=TRUE>>=
## read in 10 BRCA IDATs 
idatPath <- system.file('extdata/idat',package='TCGAMethylation450k')
mset450k <- methylumIDAT(getBarcodes(path=idatPath), idatPath=idatPath)
sampleNames(mset450k) <- paste0('TCGA', seq_along(sampleNames(mset450k)))
show(mset450k)
@

Note that the default is to collect opposite-channel fluorescence from Type I 
methylation probes (which are paired and designed to fluoresce in one channel)
in the matrices 'methylated.OOB' and 'unmethylated.OOB' (OOB, as in out-of-band)
for use in background correction and perhaps additional steps.  This also allows
a user to coerce the resulting object into minfi's RGChannelSet if desired since
all of the signal information in the IDATs is thus retained. 
\clearpage

\section{Negative and normalization controls}
Plot the negative and normalization controls:

\begin{figure}[h!]
\centering
<<controls, fig.width=5, fig.height=7, quiet=TRUE, echo=TRUE, cache=FALSE>>=
library(ggplot2)
## for larger datasets, the by.type argument be set to FALSE 
## positional effects will manifest as a wave-like pattern
p <- qc.probe.plot(mset450k, by.type=TRUE)
print(p)
@
\caption{Some of the controls on the 450k chip}
\label{fig:controlplot}
\end{figure}            

\clearpage
\section{Preprocessing the raw data}

After importing the data from IDATs, the next step is to background correct and 
dye bias equalize the data.  The default for background correction is a normal-
exponential model which uses the out-of-band intensities as control probes. Dye 
bias correction is performed by picking the least-biased sample, and using it as
a reference for red:green intensity ratio adjustments based on the normalization
controls.  Other approaches to preprocessing (as implemented in minfi and lumi) 
include various flavors of quantile normalization and smoothing spline fits. 

After preprocessing, we can reduce the size of the resulting MethyLumiSet 
substantially by dropping the out-of-band intensities with stripOOB().  This 
frees up some memory, but precludes later coercion to an RGChannelSet.

<<preprocess, eval=TRUE>>=
mset450k.proc <- stripOOB(normalizeMethyLumiSet(methylumi.bgcorr(mset450k)))
@

Now we compare the post-processing controls with those from figure 1.

\begin{figure}[h!]
\centering
<<controls2, fig.width=5, fig.height=7, quiet=TRUE, echo=TRUE, cache=FALSE>>=
library(ggplot2)
p2 <- qc.probe.plot(mset450k.proc, by.type=TRUE)
print(p2)
@
\caption{Controls after preprocessing}
\label{fig:controlplot2}
\end{figure}            

\clearpage

\section{Coercions to other data structures}

Coercions are provided to and from various data structures in the lumi and 
minfi packages.  Each provides various functionality and exhibits different 
design decisions.  One may be more appropriate than the other for some needs.
Preprocessing in methylumi retains SNP probes, which can identify label swaps,
but is less efficient than preprocessing in minfi, and cannot use shinyMethyl.

Coercing to lumi (e.g. for lumiMethyN or similar):

<<coerceLumi, eval=TRUE>>=
suppressPackageStartupMessages(require(lumi))
mset450k.lumi <- as(mset450k.proc, 'MethyLumiM')
show(mset450k.lumi)
@ 
\clearpage

Coercing back to a MethyLumiSet:

<<coerceBack, eval=TRUE>>=
mset450k.andBack <- as(mset450k.lumi, 'MethyLumiSet')
show(mset450k.andBack)
@

\clearpage
MethyLumiSet objects with OOB matrices can be coerced to RGChannelSet objects
for further processing using functions found in the minfi or ChAMP packages.

<<coerceMinfi, eval=TRUE>>=
suppressPackageStartupMessages(require(FDb.InfiniumMethylation.hg19))
rgSet450k <- as(mset450k, 'RGChannelSet')
show(rgSet450k)
@

The above will not work for the processed data, but only because we called 
stripOOB() on the resulting object to reduce its size.  If you plan on using
a preprocessed MethyLumiSet in minfi for further processing, don't strip it.

The GenomicMethylSet and GenomicRatioSet classes in minfi inherit from the 
RangedSummarizedExperiment class, which has some particularly useful features:

<<coerceMinfi2, eval=TRUE>>=
suppressPackageStartupMessages(require(minfi))
suppressPackageStartupMessages(require(IlluminaHumanMethylation450kanno.ilmn12.hg19))
grSet450k <- mapToGenome(mset450k.andBack)

sexChroms <- GRanges( seqnames=c('chrX','chrY'),
                      IRanges(start=c(1, 1), 
                              end=c(155270560, 59373566)),
                      strand=c('*','*') )
summary(subsetByOverlaps(grSet450k, sexChroms))
dim(subsetByOverlaps(grSet450k, sexChroms))
@

\clearpage

These SummarizedExperiment-derived objects can be subsetted by nearly anything 
that has an interval-based representation.  Here we extract some promoters, but
one could just as easily use AnnotationHub resources to find CTCF peaks or, say,
H3K4me1 peaks in ChIP-seq data (often associated with transcriptional enhancers;
the presence or absence of DNA methylation may help determine their activity).

<<subsetMinfi, eval=TRUE>>=
## perhaps more topical:
suppressPackageStartupMessages(require(TxDb.Hsapiens.UCSC.hg19.knownGene))
suppressPackageStartupMessages(require(Homo.sapiens))
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

KDM6AEntrezID=org.Hs.egSYMBOL2EG[['KDM6A']]
txs.KDM6A <- transcriptsBy(txdb, 'gene')[[KDM6AEntrezID]]
tss.KDM6A <- unique(resize(txs.KDM6A, 1, fix='start')) ## two start sites
promoters.KDM6A <- flank(tss.KDM6A, 100) ## an arbitrary distance upstream
show( subsetByOverlaps(grSet450k, promoters.KDM6A) ) ## probes in this window

@

Consult the AnnotationHub package vignette for some other possibilities.  If you
are unfamiliar with the powerful GenomicRanges and GenomicFeatures packages, you
may want to familiarize yourself with them as well.  

\clearpage
\section{sessionInfo}

<<results='asis'>>=
toLatex(sessionInfo())
@ 

\end{document}

