%\VignetteIndexEntry{VanillaICE Vignette}
%\VignetteKeywords{copy number, genotype, SNP}
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\newcommand{\hmmoptions}{\Robject{HmmOptions}}
\newcommand{\hmmparam}{\Robject{HmmParameter}}
\newcommand{\crlmm}{\Rpackage{crlmm}}
\newcommand{\oligo}{\Rpackage{oligo}}

\newcommand{\cne}{\widehat{\text{CN}}}
\newcommand{\gte}{\widehat{\text{GT}}}
\newcommand{\gtehom}{\widehat{\text{HOM}}}
\newcommand{\gtehet}{\widehat{\text{HET}}}
\newcommand{\pgte}{\text{S}_{\widehat{\text{\tiny GT}}}}
\newcommand{\pcne}{\text{S}_{\widehat{\text{\tiny CN}}}}
\newcommand{\pgtehom}{\text{S}_{\widehat{\text{\tiny HOM}}}}
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\begin{document}

\title{\ice{}: Hidden Markov Models for the Assessment of Chromosomal
  Alterations using High-throughput SNP Arrays}
\author{Robert Scharpf}
\maketitle


<<setup, echo=FALSE>>=
options(width=70)
@


\begin{abstract}
  This package provides an implementation of a hidden Markov Model to
  identify copy number alterations from high throughput SNP arrays.

\end{abstract}


\section{From processed SNP summaries}

The starting point for this section of the vignette are B allele
frequencies and log R ratios that are available from software such as
GenomeStudio and the \R{} package \Rpackage{crlmm}.  In this section,
we assume that the low-level summaries are available in a plain text
file -- one file per sample.  For users of the \Rpackage{crlmm}
package for preprocessing, please refer to the
\textit{crlmmDownstream} vignette.

To illustrate the workflow for copy number analysis, this package
provides Illumina 610k array data for one Hapmap trio and one oral
cleft trio preprocessed by GenomeStudio \cite{Beaty2010}.  To keep the
size of this package small, the GenomeStudio-processed files for these
6 samples have been parsed to include only columns relevant to copy
number analyses and $\approx$ 11k markers that are spanned by or
border putative CNVs.  The code chunks provided below would be the
same if the full files were included.

<<example_data>>=
library(VanillaICE)
library(foreach)
registerDoSEQ()
extdir <- system.file("extdata", package="VanillaICE", mustWork=TRUE)
files <- list.files(extdir, pattern="FinalReport")
@

\noindent The first several lines of these files have the following
information:

{\small
\begin{verbatim}
[Header]
BSGT Version,3.3.7
Processing Date,5/2/2009 12:08 AM
Content,,Human610-Quadv1_B.bpm
Num SNPs,620901
Total SNPs,620901
Num Samples,7599
Total Samples,7599
File ,1664 of 7599
[Data]
SNP Name,Allele1 - AB,Allele2 - AB,B Allele Freq,Log R Ratio
cnvi0005126,-,-,0.0085,-0.7214
cnvi0005127,-,-,0.0081,-0.8589
cnvi0005128,-,-,0.0063,-0.164
\end{verbatim}
}

%\noindent The minimal necessary information for proceeding with a SNP
%array copy number analysis in this vignette is the name of the marker
%('SNP Name'), the B allele frequencies ('B Allele Freq'), and the log
%R ratios ('Log R ratio').  These required variables can be in any
%order and can have different labels from those listed above.
%Optionally, one can also extract the 'AB' call for allele 1 and
%allele 2 so that we can keep track of the called genotypes, though
%these columns are not strictly required.

%In addition to the 6 parsed GenomeStudio files, a file containing the
%annotation of the markers. This file can be in any format and
The physical annotation of the markers in the genome can be downloaded
from on-line resources or from annotation packages available from
Bioconductor.  Here, we provide a plain-text file containing the
genomic annotation for the markers based on build UCSC build hg18:


<<annotation_file>>=
list.files(extdir, pattern="SNP_info")
@


\noindent The annotation file contains the the name of the SNP or
nonpolymorphic marker ('Name'), an indicator for whether the marker is
a SNP ('Intensity Only'), the chromosome name ('Chr'), and the genomic
physical position ('Position'). The columns for the SNP annotation can
be in any order and have different variable labels than the file
provided with this package.  Below, we copy the header of the provided
annotation file:

{\small
\begin{verbatim}
Chr,Position,Name,Intensity Only
11,45380778,cnvi0005126,1
11,45382079,cnvi0005127,1
11,46561032,cnvi0005128,1
\end{verbatim}
}


\subsection{Organizing marker annotation}

We require that marker-level annotation is represented as a
\Rclass{GRanges}-derived class.  To read the plain text annotation
file, we use the \Rfunction{fread} provided in the
\Rpackage{data.table} package.  In addition, we define an indicator
for whether the marker is polymophic using the 'Intensity Only' flag.
The \Rclass{SnpGRanges} class created from the \Robject{fgr} object in
the following code-chunk ensures that this binary indicator is created
and can be reliably accessed in downstream processing.

<<FeatureAnnotation>>=
require(data.table)
features <- suppressWarnings(fread(file.path(extdir, "SNP_info.csv")))
fgr <- GRanges(paste0("chr", features$Chr), IRanges(features$Position, width=1),
               isSnp=features[["Intensity Only"]]==0)
fgr <- SnpGRanges(fgr)
names(fgr) <- features[["Name"]]
@

Ideally, one should also include the genome build and information on
the chromosome lengths appropriate to the build. Here, we extract the
metadata on the chromosomes using BSgenome Bioconductor package for
the hg18 build.  Finally, we sort the \Robject{fgr} object such that
the chromosomes are ordered by their \texttt{seqlevels} and the
markers are ordered by their genomic position along the chromosome.

<<seqinfo>>=
library(BSgenome.Hsapiens.UCSC.hg18)
sl <- seqlevels(BSgenome.Hsapiens.UCSC.hg18)
seqlevels(fgr) <- sl[sl %in% seqlevels(fgr)]
seqinfo(fgr) <- seqinfo(BSgenome.Hsapiens.UCSC.hg18)[seqlevels(fgr),]
fgr <- sort(fgr)
@

\subsection{Organizing the marker-level summaries}

The abbreviated plain text files included with this package and
containing log R ratios and B allele frequencies from 2 trios are
listed below.


<<sourceFiles>>=
files <- list.files(extdir, full.names=TRUE, recursive=TRUE, pattern="FinalReport")
@

We will parse these files into a specific format such that all
downstream steps for copy number estimation no longer depend on the
specific format of the source files.  At this point, we can
encapsulate the the names of the source files ('sourcePaths'), the
location of where we intend to store the parsed data ('parsedPath'),
and the genomic marker annnotation created in the preceding section
 in a single object called an \Rclass{ArrayViews}.

<<ArrayViews>>=
##
## A directory to keep parsed files
##
parsedDir <- tempdir()
views <- ArrayViews(rowRanges=fgr, sourcePaths=files, parsedPath=parsedDir)
lrrFile(views) <- file.path(parsedDir, basename(fileName(views, "lrr")))
views@bafFiles <- file.path(parsedDir, basename(fileName(views, "baf")))
views@gtFiles <- file.path(parsedDir, basename(fileName(views, "gt")))
colnames(views) <- gsub(".csv", "", colnames(views))
show(views)
@

Because the format of the source files depends on upstream software
and version number within software, our approach to parsing these
files is to read one file and to store the appropriate metadata from
this file so that subsequent files can be parsed in a similar
fashion. We use the \Rfunction{fread} to read in the first file.

<<fread>>=
## read the first file
dat <- fread(files[1])
head(dat,n=3)
@

Next, we select which columns we plan to keep. Again, the required
data for downstream processing is the name of the SNP identifier, the
log R ratios, and B allele frequencies.

<<select_columns>>=
## information to store on the markers
select_columns <- match(c("SNP Name", "Allele1 - AB", "Allele2 - AB",
                          "Log R Ratio", "B Allele Freq"), names(dat))
@

We also specify the order in which we will store the marker-level
summaries by matching the \Rfunction{rownames} of the \Robject{views}
object with the names of the markers in the source file:

<<order_of_markers>>=
index_genome <- match(names(fgr), dat[["SNP Name"]])
@

Similar to the parameter classes defined in \Rpackage{Rsamtools}, we
encapsulate the information for parsing the columns and rows of the
source files in a class.  In addition, we specify which variable names
in the source file refers to log R ratios ('cnvar'), B allele
frequences ('bafvar'), and genotypes ('gtvar').

<<scan_params>>=
scan_params <- CopyNumScanParams(index_genome=index_genome, select=select_columns,
                                 cnvar="Log R Ratio",
                                 bafvar="B Allele Freq",
                                 gtvar=c("Allele1 - AB", "Allele2 - AB"))
@


The \Rfunction{parseSourceFile} will parse a single file in the
\Robject{views} object (by default, the first file) according to the
parameters for reading the data in the \Robject{scan\_params} object
and write the output to the \Rfunction{parsedPath} directory. In
particular, the \Rfunction{parseSourceFile} returns \Rclass{NULL}.

<<applyParseSourceFile>>=
parseSourceFile(views, scan_params)
@

Apart from confirming their existance, the user should not have a need
to directly access the parsed files.  Utilities for querying these
files are provided through the \Robject{views} object.
<<list_parsed_files>>=
head(list.files(parsedPath(views)), n=3)
@

\subsection{Accessors for the parsed data}

The preference for writing the parsed data to disk rather than keeping
the data in RAM is simply that the latter does not scale to projects
involving thousands of samples. For the former, slices of the parsed
data easily be accessed from the \Rfunction{parsedPath} directory via
methods defined for the \Rclass{ArrayViews} class.  For example, one
can use accessors for the low-level summaries directly:
\Rfunction{lrr}, \Rfunction{baf}, and \Rfunction{genotypes} for log R
ratios, B allele frequencies, and genotypes, respectively.  The user
has the option of either subsetting the views object or subsetting the
matrix returned by the accessor to extract the appropriate data
slice. In the following examples, we access data on the first 2
markers.

<<Views>>=
lrr(views)[1:2, ]
## or
lrr(views[1:2, ])
## B allele frequencies
baf(views[1:2, ])
## Use :: to avoid  masking by function of the same name in crlmm
VanillaICE::genotypes(views)[1:2, ]
@

More often, it is useful to extract the low-level data in a
\Rclass{RangedSummarizedExperiment}-derived object such that meta-data on the
samples remains bound to the columns of the assay data (log R ratios /
B allele frequencies) and meta-data on the rows remains bound to the
rows of the assay data. This is accomplished by applying the
\Rfunction{SnpExperiment} function to a \Robject{views} object. In the
following example, we create a \Rclass{RangedSummarizedExperiment}-derived
object for the first three samples in the \Robject{views} object.


<<SnpArrayExperiment>>=
snp_exp <- SnpExperiment(views[, 4:5])
show(snp_exp)
@


\section{Hidden Markov model}

\subsection{HMM parameters}

The hidden Markov model for inference of germline copy number from SNP
array data was originally described in Scharpf {\it et al.}
\cite{Scharpf2008} but has evolved to focus more on B allele
frequencies than genotype call probabilities [the latter requires a
  dependency on the \Rpackage{crlmm} package].  Many of the the
updates for computing emission probabilities have been described more
recently \cite{Scharpf2012}.

Fitting the hidden Markov model to the marker-level summaries requires
extracting the relevant data from a \Robject{views} object using the
\Rfunction{SnpExperiment} function illustrated in the previous
section.  All user-level parameters relevant for fitting the HMM are
specified in a parameter object for the emission probabilities and a
parameter object for the transition probabilities.  In the following
code-chunk, we create a parameter object for the emission
probabilities.

<<emission_param>>=
param <- EmissionParam()
@

The easiest way to specify or change parameters for computing emission
probabilities is through the \Rfunction{EmissionParam} constructor.
For example, here we create a parameter object with the
\Rfunction{temper} parameter set to 1/2:

<<temper>>=
param <- EmissionParam(temper=0.5)
show(param)
@

Similarly, the constructor for the \Rclass{TransitionParam} class can
be used to specify alternatives to the defaults.  By not specifying an
\Robject{TransitionParam} object, default values created by the
constructor are used by the HMM in the following example.

\subsection{Fitting the HMM}

The function \Rfunction{hmm2} fits the 6-state HMM to the
\Robject{snp\_exp} object, returning a list-derived class (a
\Rclass{HMMList}) of the same length as the number of samples.


<<hmm>>=
fit <- hmm2(snp_exp, param)
show(fit)
length(fit)
## HMM object for the first sample
fit[[1]]
@

\section{Inspecting, Filtering, and plotting HMM results}

Several methods are defined for the \Rclass{HMMList} class to
facilitate the selection of candidate CNVs, the filtering of technical
artifacts, and to enable visualization of the HMM calls in the context
of the marker-level summaries.

The \Robject{fit} object is an instance of the \Rclass{HMMList} object
of length three, each element corresponding to a sample:

<<HMMList_names>>=
names(fit)
@

The \R{} method \verb+\\+ can be used to access the HMM summary for
the results for the jth sample. For example, here we extract the HMM
summary for the 2nd sample:

<<HMMList_subset>>=
show(fit[[2]])
@

Alternatively, we can use \Rfunction{unlist} to create a single
\Rclass{GRanges}-derived class containing the segmentation of all
three samples

<<HMMList_unlist>>=
head(unlist(fit), n=3)
@

\noindent or a \Rclass{GRangesList} by splitting on the sample id:

<<HMMList_grangeslist>>=
grl <- split(unlist(fit), unlist(fit)$id)
@

\subsection{Filters}

There are several meta-data columns stored in the
\Rclass{GRanges}-derived summary useful for filtering the set of
genomic intervals. All the available parameters for filtering the
\Robject{fit} object are stored in the parameter class
\Rclass{FilterParam} of which an instance can be created by its
constructor of the same name without any arguments.

<<filter_param>>=
filter_param <- FilterParam()
show(filter_param)
@

To apply the default filter parameters to the \Robject{fit} object, we
use the \Rfunction{cnvFilter} function. The \Rfunction{cnvFilter}
function returns only the set of genomic ranges satisfying the
filters. For example,

<<cnvFilter>>=
cnvFilter(fit, filter_param)
@

To select only the segments with altered copy number states (states 1,
2, 5, and 6) on chromosome 22, we can define the filter parameters as
follows:

<<cnvFilter_altered>>=
select_cnv <- FilterParam(state=c("1", "2", "5", "6"), seqnames="chr22")
cnvs <- cnvFilter(fit, select_cnv)
cnvs
@


\subsection{Visualization}

\subsubsection{Trellis graphics for low-level summaries}

Visualization of the CNVs in the context of the lower-level summaries
is acheived through a combination of grid and the grid-derived
graphics provided by \Rpackage{lattice}.  The \Rfunction{xyplotList}
and constructor \Rfunction{HmmTrellisParam} should be sufficient for
producing a decent graphic using the default settings. In the
following code chunk, we create a \Rclass{trellis} object for each CNV
segment.

<<xyplotList>>=
trellis_param <- HmmTrellisParam()
cnvList <- split(cnvs, cnvs$id)
figList <- xyplotList(cnvList, snp_exp, trellis_param)
names(figList)
@

\noindent Each element in \Robject{figList} is a \Rclass{trellis}
object and can be displayed using \Rfunction{print}.

<<trellis>>=
class(figList[["FinalReport6841.csv"]][[1]])
@


\subsubsection{Layout using grid}

<<viewports>>=
fig1 <- figList[["FinalReport6841.csv"]][[1]]
@

<<fig1,fig=TRUE, width=8, height=6,include=FALSE>>=
vps <- viewports()
xygrid(fig1, vps, cnvList[[1]][1])
@

\begin{figure}[t]
  \begin{center}
  \includegraphics[width=0.8\textwidth]{VanillaICE-fig1}
  \caption{\label{fig:fig1} A single-copy duplication (state 5).}
  \end{center}
\end{figure}

A hemizygous deletion on chromosome 22 is split into too many regions.

<<fig2,fig=TRUE, width=8, height=6>>=
cnvs_sample2 <- cnvList[[2]]
cnvs_sample2
xygrid(figList[[2]][[1]], vps, cnvs_sample2[1])
@

Combining the adjacent hemizygous deletions through \Rfunction{reduce}
provides a more satisfying segmentation of this data.

<<reduce>>=
cnvs_sample2r <- reduce(cnvs_sample2, min.gapwidth=500e3)
fig2 <- xyplotList(cnvs_sample2r, snp_exp)
@

<<fig_reduced, fig=TRUE, width=8, height=6, include=FALSE, echo=FALSE>>=
invisible(print(fig2[[1]]))
@

\begin{figure}[t]
  \begin{center}
  \includegraphics[width=0.8\textwidth]{VanillaICE-fig_reduced}
  \caption{\label{fig:fig2} A hemizygous deletion (state 2) on
    chromosome 22 after merging adjacent hemizygous CNV calls.}
  \end{center}
\end{figure}

\section*{Parallelization}

As the HMM is fit independently to each sample, parallelization is
straightforward.  In the following unevaluated code chunk, we set up a
parallel environment using the \R{} packages \Rpackage{snow} and
\Rpackage{foreach}.

<<parallelEnvironment,eval=FALSE>>=
library(foreach)
library(snow)
library(doSNOW)
cl <- makeCluster(2, type="SOCK")
registerDoSNOW(cl)
@

<<fitParallel, eval=FALSE>>=
results <- hmm2(snp_exp)
@

<<stopcl,eval=FALSE>>=
stopCluster(cl)
@

\section*{Citing this software}
% \bibitem{Scharpf2008}
Robert~B Scharpf, Giovanni Parmigiani, Jonathan Pevsner, and Ingo Ruczinski.
\newblock Hidden {M}arkov models for the assessment of chromosomal alterations
  using high-throughput {SNP} arrays.
\newblock {\em Annals of Applied Statistics}, 2(2):687--713, 2008.


\section*{Session Information}

The version number of R and packages loaded for generating the vignette
were:

<<echo=FALSE, results=tex>>=
toLatex(sessionInfo())
@

\bibliography{ice}{}
\bibliographystyle{plain}

\end{document}
