%\VignetteEngine{knitr::knitr}
%\VignetteIndexEntry{EGSEA vignette}
%\VignettePackage{EGSEA}

\documentclass[11pt]{article}
<<style-knitr, eval=TRUE, echo=FALSE, results="asis">>=
BiocStyle::latex()
@

\usepackage{url}
\usepackage{subcaption}

\begin{document}
\bioctitle[EGSEA]{Ensemble of Gene Set Enrichment Analyses}
\author{Monther Alhamdoosh\footnote{m.hamdoosh@gmail.com}, Milica Ng and Matthew
Ritchie\footnote{mritchie@wehi.edu.au}}

\maketitle
\tableofcontents


\newpage


\section{Introduction}
The \Biocpkg{EGSEA} package implements the Ensemble of Gene Set Enrichment
Analysis (EGSEA) algorithm that utilizes the analysis results of twelve
prominent GSE algorithms in the literature to calculate collective significance
scores for each gene set. These methods include: \Rfunction{ora}
\cite{Tavazoie1999}, \Biocpkg{globaltest} \cite{Goeman2004}, \Rfunction{plage}
\cite{Tomfohr2005}, \Biocpkg{safe} \cite{Barry2005}, \Rfunction{zscore} \cite{Lee2008},
\Biocpkg{gage} \cite{Luo2009}, \Rfunction{ssgsea} \cite{Barbie2009},
\Rfunction{roast}, \Rfunction{fry} \cite{Wu2010}, \Biocpkg{PADOG}
\cite{Tarca2012}, \Rfunction{camera} \cite{Wu2012} and \Biocpkg{GSVA} \cite{Hanzelmann2013}. The
\Rfunction{ora}, \Rfunction{gage}, \Rfunction{camera} and \Rfunction{gsva}
methods depend on a competitive null hypothesis while the remaining eight
methods are based on a self-contained null hypothesis. Conveniently,
\Biocpkg{EGSEA} is not limited to these twelve GSE methods and new GSE tests can be easily
integrated into the framework. The plage, zscore and ssgsea algorithms are
implemented in the \Biocpkg{GSVA} package and \Rfunction{camera}, \Rfunction{fry} and
\Rfunction{roast} are implemented in the \Biocpkg{limma} package.
\Biocpkg{EGSEA} was implemented with parallel computation enabled using the
\CRANpkg{parallel} package. There are two levels of parallelism in EGSEA:(i)
parallelism at the method-level and (ii) parallelism at the experimental
contrast level. A wrapper function was written for each individual GSE method
to utilize existing R and Bioconductor packages and create a universal interface
for all methods. The \textit{ora} method was implemented using the
\Rfunction{phyper} function from the \CRANpkg{stats} package, which estimates the hypergeometric
distribution for a $2 \times 2$ contingency table.

\par RNA-seq reads are first aligned to the reference genome and mapped reads
are assigned to annotated genomic features to obtain a summarized \textbf{count
matrix}. The \Biocpkg{EGSEA} package was developed so that it can accept a count
matrix or a \Robject{voom} object. Most of the GSE methods were intrinsically designed to
work with microarray expression values and not with RNA-seq counts, hence the
\Rfunction{voom} transformation is applied to the count matrix to generate an
expression matrix applicable for use with these methods \cite{Law2014} . Since
gene set tests are most commonly applied when two experimental conditions are
compared, a design matrix and a contrast matrix are used to construct the
experimental comparisons of interest. The target collection of gene sets is
indexed so that the gene identifiers can be substituted with the indices of
genes in the rows of the count matrix. The GSE analysis is then carried out by
each of the selected methods independently and an FDR value is assigned to each
gene set. Lastly, the ensemble functions are invoked to calculate collective
significance scores for each gene set.

\par The \Biocpkg{EGSEA} package also allows for performing
the over-representation analysis on the EGSEA gene set collections that were
adopted from MSigDB, KEGG and GeneSetDB databases. 


\section{Citation}
\label{sec:citation}
\begin{itemize}
  \item Alhamdoosh, M., Ng, M., Wilson, N. J., Sheridan, J. M., Huynh, H.,
  Wilson, M. J., Ritchie, M. E. (2016). Combining multiple tools outperforms
  individual methods in gene set enrichment analyses. bioRxiv.
\end{itemize}


\section{Installation instructions}
The \Biocpkg{EGSEA} package was developed so that it harmonizes with the
existing R packages in the CRAN repository and the Bioconductor project. 

\subsection{System prerequistes}
\Biocpkg{EGSEA} does not require any software package or library to be installed before it
can be installed regardless of the operating system.

\subsection{R package dependencies}
The \Biocpkg{EGSEA} package depends on several R packages that are not in the
Bioconductor project. These packages are listed below:

\begin{itemize}
\item \CRANpkg{HTMLUtils} facilitates automated HTML report creation, in
particular framed HTML pages and dynamically sortable tables. It is used in
\Biocpkg{EGSEA} to generate the stats tables. To install it, type in the R
console 

\par \Rcode{install.packages("HTMLUtils")}

\item \CRANpkg{hwriter} has easy-to-use and versatile functions to output R
objects in HTML format. It is used in this package to create the HTML pages of
the EGSEA report.
To install it, 

\par \Rcode{install.packages("hwriter")}

\item \CRANpkg{ggplot2} is an implementation of the grammar of graphics in R. It
is used in this package to create the summary plots. To install it, type  

\par \Rcode{install.packages("ggplot2")}

\item \CRANpkg{gplots} has various R programming tools for plotting data. It is
used in \Biocpkg{EGSEA} to create heatmaps. To install it, run

\par \Rcode{install.packages("gplots")}

\item \CRANpkg{stringi} allows for fast, correct, consistent, portable, as well
as convenient character string/text processing in every locale and any native
encoding. It is used in generating the HTML pages. To install this package, type

\par \Rcode{install.packages("stringi")}

\item \CRANpkg{metap}  provides a number of methods for
meta-analysis of significance values. To install this package, type

\par \Rcode{install.packages("metap")}

\item \CRANpkg{parallel} handles running much larger chunks of computations in
parallel. It is used to carry out gene set tests on parallel. It is usually
installed with R. 

\item \CRANpkg{devtools} is needed to install packages from Bitbucket. 
It is available at CRAN. For Windows this seems to depend on
having Rtools for Windows installed. You can download and install this from:
\url{http://cran.r-project.org/bin/windows/Rtools/}. To install
\CRANpkg{devtools}, run in R console 

\par \Rcode{install.packages("devtools")}
 
\end{itemize}

\subsubsection{Bioconductor packages}
The Bioconductor packages that need to be installed in order for
\Biocpkg{EGSEA} to work properly are:
\Biocpkg{PADOG}, \Biocpkg{GSVA}, \Biocpkg{AnnotationDbi}, \Biocpkg{topGO},
\Biocpkg{pathview}, \Biocpkg{gage}, \Biocpkg{globaltest}, \Biocpkg{limma},
\Biocpkg{edgeR}, \Biocpkg{safe}, \Biocpkg{org.Hs.eg.db}, \Biocpkg{org.Mm.eg.db},
\Biocpkg{org.Rn.eg.db}. They can be installed from Biocondcutor using
the following commands in R console

<<echo=TRUE,  eval=FALSE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
source("http://www.bioconductor.org/biocLite.R")
biocLite(c("PADOG", "GSVA", "AnnotationDbi", "topGO", "pathview", "gage",
"globaltest", "limma", "edgeR", "safe", "org.Hs.eg.db", "org.Mm.eg.db",
"org.Rn.eg.db"))
@


\subsubsection{EGSEAdata: essential data package}
The gene set collections that are used by \Biocpkg{EGSEA} were preprocessed
and converted into R data objects to be used by the EGSEA functions. The data
objects are stored in an R package, named \Biocpkg{EGSEAdata}. It contains the
gene set collections that are needed by \Biocpkg{EGSEA} to perform gene set
testing. \Biocpkg{EGSEAdata} is available at Bioconductor and can be also
installed from Bitbucket.

\par \Biocpkg{EGSEAdata} can be installed from Bioconductor by running in R
console the following commands 
<<echo=TRUE,  eval=FALSE,tidy=TRUE>>=
source("http://bioconductor.org/biocLite.R")
biocLite("EGSEAdata")
@

It can be also installed from Bitbucket from inside R console using the
\Rpackage{devtools} package as follows

<<echo=TRUE,  eval=FALSE,tidy=TRUE>>= 
library(devtools) 
install_bitbucket("malhamdoosh/egseadata", ref="Stable_Release")
@ 

\subsection{Installation}
\Biocpkg{EGSEA} can be installed from the Bioconductor project or the Bitbucket
repository. We aim to only push the successfully tested versions to
Bioconductor. Therefore, the Bitbucket version can have additional features that
are not yet available in Bioconductor. 

\subsubsection{Bioconductor}
To install the release version of \Biocpkg{EGSEA} from Bioconductor, type in R
console

<<echo=TRUE,  eval=FALSE,tidy=TRUE>>=
source("http://bioconductor.org/biocLite.R")
biocLite("EGSEA")
@

To install the developmental version of \Biocpkg{EGSEA} from Bioconductor, run the
following commands in R console

<<echo=TRUE,  eval=FALSE,tidy=TRUE>>=
library(BiocInstaller)
useDevel()
biocLite("EGSEA")
@

\subsubsection{Bitbucket}

To install the developmental version of \Biocpkg{EGSEA} from Bitbucket, type in the R
console

<<echo=TRUE,  eval=FALSE,tidy=TRUE>>=
library(devtools)
install_bitbucket("malhamdoosh/egsea", ref="Devel_Release")
@

The stable release version of \Biocpkg{EGSEA} can be obtained from Bitbucket by
setting \Rcode{ref = "Stabel\_Release"} in the previous commands.

\section{Quick start}
\subsection{EGSEA gene set collections}
The Molecular Signatures Database (MSigDB) \cite{Subramanian2005} v5.0 was
downloaded from \url{http://www.broadinstitute.org/gsea/msigdb} (05 July 2015,
date last accessed) and the human gene sets were extracted for each collection
(h, c1, c2, c3, c4, c5, c6, c7). Mouse orthologous gene sets of these MSigDB
collections were adopted from 
\url{http://bioinf.wehi.edu.au/software/MSigDB/index.html} \cite{Wu2012}.
EGSEA uses Entrez Gene identifiers \cite{Maglott2005} and alternate gene
identifiers must be first converted into Entrez IDs. KEGG pathways
\cite{Kanehisa2000} for mouse and human were downloaded using the
\textit{gage} package. To extend the capabilities of EGSEA, a third database of
gene sets was downloaded from the GeneSetDB \cite{Araki2012}
\url{http://genesetdb.auckland.ac.nz/sourcedb.html} project. In total, more
than 25,000 gene sets have been collated along with annotation information for
each set (where available).

\par  The \Biocpkg{EGSEA} package has four indexing functions that utilize the
gene set collections of \Biocpkg{EGSEAdata}. They map the Entrez gene
IDs of the input dataset into the
gene sets of each collection and create an index for each collection. These
fucntions also extract annotation information from \Biocpkg{EGSEAdata} for each
gene set to be displayed within the EGSEA HTML report. These functions are as
follow
\begin{itemize}
  \item \Rfunction{buildKEGGIdx} builds an index for the KEGG pathways
  collection and loads gene set annotation. Type ?buildKEGGIdx in the console to
  see how to use this function.
  
  \item \Rfunction{buildMSigDBIdx} builds indexes for the MSigDB gene set
  collections and loads gene set annotation. Type ?buildMSigDBIdx in the console
  to see how to use this function.
  
  \item \Rfunction{buildGeneSetDBIdx} builds indexes for the GeneSetDB
  collections and loads gene set annotation. Type ?buildGeneSetDBIdx
  in the console to see how to use this function.
  
  \item \Rfunction{buildIdx} is one-step method to build indexes for
  collections selected from the KEGG, MSigDB and GeneSetDB databases.
  Type ?buildIdx in the console to see how to use this function.
  
\end{itemize}

\par These four functions take a vector of Entrez Gene IDs and the species
name and return an object (or list of objects) of class
\Rclass{GSCollectionIndex}.

\textbf{Note:} To use the \Rclass{GSCollectionIndex} objects with the other
\Biocpkg{EGSEA} functions, the order of input ids vector should match that of the row names of the count matrix or the \Robject{voom} object.

\subsection{EGSEA on a human dataset}
The \Biocpkg{EGSEA} package basically performs gene set enrichment analysis on
a \Robject{voom} object generated by the \Rfunction{voom} function from the
\Biocpkg{limma} package. Actually, it was primarily developed to extend the
limma-voom RNA-seq analysis pipeline. To quickly start with \Biocpkg{EGSEA}
analysis, an example on analyzing a human IL-13 dataset is presented here. 

\par This experiment aims to identify the biological pathways and diseases
associated with the cytokine Interleukin 13 (IL-13) using gene expression measured in peripheral blood mononuclear cells
(PBMCs) obtained from 3 healthy donors. The expression profiles of \textit{in
vitro} IL-13 stimulation were generated using RNA-seq technology for $3$ PBMC
samples at $24$ hours. The transcriptional profiles of PBMCs without IL-13
stimulation were also generated to be used as controls. Finally, an
IL-13R$\alpha$1 antagonist was introduced into IL-13
stimulated PBMCs and the gene expression levels after 24h were profiled to
examine the neutralization of IL-13 signaling by the antagonist. Only two
samples were available for the last condition. Single-end 100bp reads were
obtained via RNA-seq from total RNA using a HiSeq 2000 Illumina sequencer.
TopHat was used to map the reads to the human reference genome (GRCh37.p10).
HTSeq was then used to summarize reads into a gene-level count matrix. The TMM
method from the \Biocpkg{edgeR} package was used to normalize the RNA-seq
counts. Data are available from the GEO database \url{www.ncbi.nlm.nih.gov/geo/}
as series GSE79027.

\par To perform EGSEA analysis on this dataset, the \Biocpkg{EGSEA} package is
first loaded follow

<<echo=TRUE,  eval=TRUE,tidy=TRUE, message=F, warning=F>>=
library(EGSEA)
@

Then, the \Robject{voom} data object of this experiment is
loaded from \Biocpkg{EGSEAdata} as follows  

<<echo=TRUE,  eval=TRUE,tidy=TRUE>>=
library(EGSEAdata)
data(il13.data)
v = il13.data$voom
names(v)
v$design
contrasts = il13.data$contra
contrasts
@
A detailed explanation on how a \Robject{voom} can be created from a raw
RNA-seq count matrix can be found in this workflow article \cite{Law2016}.

\par Before the EGSEA pipeline is invoked, gene set collections need to be
pre-processed and indexed using the EGSEA indexing functions as it was mentioned
earlier. Here, indexes for the KEGG pathways and the c5 collection
from the MSigDB are created as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>= 
gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human", msigdb.gsets="c5", 
 			kegg.exclude = c("Metabolism"))
names(gs.annots)
@

The \Robject{gs.annots} is a list of two objects of class
\Rclass{GSCollectionIndex} that are labelled with "kegg" and "c5".

A quick summary of the collection indexes can be displayed using the
\Rfunction{summary} function as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
summary(gs.annots$kegg)
summary(gs.annots$c5)
@
This shows the name, label and number of gene sets in the KEGG collection. Next,
we select the base methods of the EGSEA analysis

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
baseMethods = egsea.base()[-c(2, 12)]
baseMethods
@

Another important parameter for the EGSEA analysis is the \Rcode{sort.by}
argument which determines how the gene sets are ordered. The possible values of
this argument can be seen as follows
<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
egsea.sort()
@

Finally, the EGSEA analysis can be performed using the \Rfunction{egsea}
function as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
# perform the EGSEA analysis
# set report = TRUE to generate HTML report.
# set display.top = 20 to display more gene sets. It takes longer time to run.
gsa = egsea(voom.results=v, contrasts=contrasts,  gs.annots=gs.annots, 
 			symbolsMap=v$genes, baseGSEAs=baseMethods,
            egsea.dir="./il13-egsea-report",
 			 sort.by="avg.rank", num.threads = 4, report=FALSE)
@

The function \Rfunction{egsea} returns an object of class \Rclass{EGSEAResults},
which is described next in Section \ref{sec:s4_classes}. To generate an HTML report of
the EGSEA analysis results, you need to set \Rcode{report=TRUE}. Then, the EGSEA
report can be launched by opening \url{./il13-egsea-report/index.html}. A quick
summary of the top ten significant gene sets from each collection and for each
contrast including the comparative analysis, if there are more than one
contrast, can be displayed using the \Rfunction{summary} function as follows 

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
summary(gsa)
@

\par To run the EGSEA analysis with all the gene set collections
that are avilable in the \Biocpkg{EGSEAdata} package, use the
\Rfunction{buildIdx} function to create the gene set indexes as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
gs.annots = buildIdx(entrezIDs=rownames(v$E), species="human", gsdb.gsets="all")
names(gs.annots)
@

\section{S4 classes and methods}
\label{sec:s4_classes}

\begin{figure}[!h]
\center
\includegraphics[width=0.8\paperwidth]{egsea_classes-crop.pdf}
\caption{The S4 classes and methods of \Biocpkg{EGSEA}.}
\label{fig:egsea_classes}
\end{figure}

\Rpackage{EGSEA} implements two S4 classes to perform its functionalities
efficiently. The \Rclass{GSCollectionIndex} stores an indexed gene set
collection, which can be used to perform an EGSEA analysis, and the
\Rclass{EGSEAResults} stores the results of an EGSEA analysis. Each class has
several slots and S4 methods to enable the user explore EGSEA results
efficiently and effectively (Figure \ref{fig:egsea_classes}). 

The \Rclass{GSCollectionIndex} class has seven slots and four S4 methods
that are defined as follows
\begin{itemize}
  \item \Rclass{GSCollectionIndex} slots:
  \begin{itemize}
    \item \Robject{original} is a list of character vectors, each stores the
    Entrez Gene IDs of a gene set.
    \item \Robject{idx} is a list of character vectors, each stores only the
    indexes of the mapped genes of a set. 
    \item \Robject{anno} is a data frame that stores additional annotation for
    each gene set. 
    \item \Robject{featureIDs} is a character vector of the Entrez Gene IDs that
    were used to index the gene sets. 
    \item \Robject{species} is a character that stores the species name. It
    accepts 
    \item \Robject{name} is a character that stores a short description of the
    gene set collection. 
    \item \Robject{label} is a character that stores a label for the collection
    to identify it from other collections when multiple collections are used for
    an EGSEA analysis. 
  \end{itemize}
  \item \Rclass{GSCollectionIndex} S4 methods: 
  \begin{itemize}
      \item \Rfunction{show} displays the content of the gene set collection. 
      \item \Rfunction{summary} displays a brief summary of the gene set
      collection.
      \item \Rfunction{getSetByName} returns a list of the details of gene sets
      given their names.
      \item \Rfunction{getSetByID} returns a list of the details of gene sets
      given their IDs.
   \end{itemize}
\end{itemize}

The \Rclass{EGSEAResults} class has eleven slots and ten S4 methods
that are defined as follows
\begin{itemize}
  \item \Rclass{EGSEAResults} slots: 
  \begin{itemize}
      \item \Robject{results} is a list that stores the EGSEA analysis results
      in a hierarchical format (Figure \ref{fig:egsea_results}). The
      \textit{comparison} element only exists when more than one contrast are
      analyzed. The \textit{ind.results} only exists if the
      EGSEA function argument \Rcode{print.base = TRUE}.  
      \item \Robject{limmaResults} is a limma linear fit model. This is only
      defined when \Rcode{keep.limma = TRUE}.
      \item \Robject{contrasts} is a character vector of contrast names. 
      \item \Robject{sampleSize} is a numeric value of the number of samples. 
      \item \Robject{gs.annots} is a list of objects of class 
      \Rclass{GSCollectionIndex} that stores the indexed gene set collections
      that were used in the EGSEA analysis.
      \item \Robject{baseMethods} is a character vector of the base GSE methods
      that were used in the EGSEA analysis. 
      \item \Robject{baseInfo} is a list that stores additional information on
      the base methods (e.g., version).
      \item \Robject{combineMethod} is a character value of the name of p-value
      combinging method. 
      \item \Robject{sort.by} is a character value of the sorting EGSEA score. 
      \item \Robject{symbolsMap} is a data frame of two columns that stores the
      mapping of the Entrez Gene IDs to their gene symbols. 
      \item \Robject{logFC} is a matrix of the calculated (or provided) logFC
      values where columns correspond to contrasts and rows correspond to genes.
      \item \Robject{report} is a logical value indicates whether an HTML report
      was generated or not.
      \item \Robject{report.dir} is a character value of the HTML report
      directory (if it was generated). 
   \end{itemize}
   \item \Rclass{EGSEAResults} S4 methods:
   \begin{itemize}
      \item \Rfunction{show} displays the parameters of the EGSEAResults object.
      \item \Rfunction{summary} displays a brief summary of the EGSEA analysis
      results.
      \item \Rfunction{topSets} extracts a table of the top-ranked gene sets
      from an EGSEA analysis.
      \item \Rfunction{plotSummary} generates a Summary plot of an EGSEA
      analysis for a given gene set collection and a selected contrast. 
      \item \Rfunction{plotMethods} generates a multi-dimensional scaling (MDS) plot
      for the gene set rankings of the base methods of an EGSEA analysis.
      \item \Rfunction{plotHeatmap} generates a heatmap of fold changes for a
      selected gene set.  
      \item \Rfunction{plotPathway} generates a visual map for a selected KEGG
      pathway. 
      \item \Rfunction{showSetByName} displays the details of gene sets
      given their names and their collection.
      \item \Rfunction{showSetByID} displays the details of gene sets
      given their IDs and their collection.
      \item \Rfunction{limmaTopTable} returns a dataframe of the top table of
      the limma analysis for a given contrast. This is only
      defined when \Rcode{keep.limma = TRUE}.
      \item \Rfunction{getlimmaResults} returns the linear model fit produced by
      \Rfunction{limma::eBayes}. This is only
      defined when \Rcode{keep.limma = TRUE}.
      \item \Rfunction{getSetScores} returns a dataframe of the gene set
      enrichment scores per sample. This can be only calculated using specific 
      base methods, namely, "ssgsea". This is only defined when
      \Rcode{keep.set.scores = TRUE}.
      \item \Rfunction{plotSummaryHeatmap} generates a summary heatmap for the
      top n gene sets of the comparative analysis of multiple contrasts. 
   \end{itemize}
\end{itemize}

\begin{figure}[!h]
\center
\includegraphics[width=0.8\paperwidth]{egsea_results-crop.pdf}
\caption{The structure of the slot \Rcode{results} of the
class \Rclass{EGSEAResults}.}
\label{fig:egsea_results}
\end{figure}

Next, we show how these different methods can be used to query the EGSEA
results. To obtain a quick overview of the parameters of IL-13 EGSEA analysis    

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
show(gsa)
@

The EGSEA analysis results can be queried in different ways. For example, the
top 10 gene sets of the KEGG collection for the contrast X24IL13-X24 can be
retrieved as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>=
topSets(gsa, contrast=1, gs.label="kegg", number = 10)
@
Here the gene sets are ordered based on the value of the argument
\Rcode{sort.by} when the EGSEA analysis was invoked, i.e., the \textit{avg.rank} in this example.
However, the top gene sets based on a selected EGSEA score, e.g. ORA ranking,
can be retreieved as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>=
t = topSets(gsa, contrast=1, gs.label="c5", sort.by="ora", number = 10, names.only=FALSE)
t
@

This can be useful to identify over-represented GO terms since GO gene sets in
the c5 collection are based on ontologies which do not necessarily comprise
co-regulated genes. More information on the first gene set can be retrieved
as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>=
showSetByName(gsa, "c5", rownames(t)[1])
@

The \textit{NumGenes} shows the number of your dataset genes that were mapped to
this gene set out of the total number of genes in the set. This ratio mainly
depends on the filtering criteria that are used for constructing the count
matrix. 

Similarly, the top gene sets of the comparative analysis can
be retrieved as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>=
t = topSets(gsa, contrast="comparison", gs.label="kegg", number = 10)
t
@

More information on the first gene set of the comparative analysis can be
retrieved as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>=

showSetByName(gsa, "kegg",  rownames(t)[1])

@

Next, the visualization capabilities of EGSEA are explored. The results can be
visualized at the experiment-level using the MDS plot, Summary or GO Graph
plots, or at the set-level using heatmaps and pathway maps. 

The performance of the EGSEA base methods on a selected contrast can be
visualized usign an MDS plot that shows how different methods rank a gene set
collection (Figure \ref{fig:summary_methods}). For example, the performance of
the various methods on the contrast X24IL13-X24 and the KEGG collection can be
plotted as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
plotMethods(gsa, gs.label = "kegg", contrast=1, file.name="X24IL13-X24-kegg-methods")
@

\begin{figure}[!h]
\center
\includegraphics[width=0.6\paperwidth]{X24IL13-X24-kegg-methods.pdf}
\caption{The performance of multiple GSE methods on the contrast X24IL13-X24.}
\label{fig:summary_methods}
\end{figure}

The overall EGSEA significance of all gene sets in a given collection and a
selected contrast can be visualized using the summary plots (Figure
\ref{fig:kegg_summary}) as follows 

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
plotSummary(gsa, gs.label="kegg", contrast = 1, file.name="X24IL13-X24-kegg-summary")
@

\begin{figure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{{X24IL13-X24-kegg-summary.dir}.pdf}
\caption{\label{fig:kegg_summary_dir} Directional summary plot}
\end{subfigure}
\begin{subfigure}{.5\textwidth}
\centering
\includegraphics[width=\linewidth]{{X24IL13-X24-kegg-summary.rank}.pdf}
\caption{\label{fig:kegg_summary_rank} Ranking summary plot }
\end{subfigure}
\caption{Summary plots for the contrast X24IL13-X24 on the KEGG pathways
collection.}
\label{fig:kegg_summary}
\end{figure}

Gene set IDs are used to highlight significant sets on the Summary plot. To
obtain additional information on these gene sets, the function
\Rfunction{showSetByID} can be used as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
showSetByID(gsa, gs.label="kegg", c("hsa04060", "hsa04640"))
@

Gene Ontology (GO) graphs can be generated for the three categories of GO terms:
Biological Process (BP), Molecular Function (MF) and Cellular Componenet (CC).
There are two GO term collections in the package \Biocpkg{EGSEAdata}: c5 from
MSigDB and gsdbgo from GeneSetDB. To generate the GO graphs for c5 collection on
the contrast X24IL13-X24 
<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
plotGOGraph(gsa, gs.label="c5", file.name="X24IL13-X24-c5-top-", sort.by="avg.rank")
@
This command generates three graphs, one for each GO category and, by default,
displays the top 5 significant terms in each category. For example, Figure
\ref{fig:go_terms} shows the BP graph. 

\begin{figure}[!h]
\center
\includegraphics[width=0.8\paperwidth]{X24IL13-X24-c5-top-BP.pdf}
\caption{The top significant Biological Processes (BP) from the c5 collection.}
\label{fig:go_terms}
\end{figure}

Heatmaps of the gene fold changes can be gereated for a selected gene set as
follows
<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
plotHeatmap(gsa, "Asthma", gs.label="kegg", contrast=1,
        file.name="asthma_hm")
@

\begin{figure}[!h]
\center
\includegraphics[width=0.6\paperwidth]{asthma_hm.pdf}
\caption{Asthma heatmap for the contrast X24IL13-X24}
\label{fig:heatmaps}
\end{figure}

Figure \ref{fig:heatmaps} shows the Asthma gene set heatmap. For the KEGG
collection, a pathway map that shows the gene interactiosn can be generated as
follows 

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
plotPathway(gsa, "Asthma", gs.label="kegg", file.name="asthma_pathway")
@

\begin{figure}[!h]
\center
\includegraphics[width=0.8\paperwidth]{asthma_pathway.png}
\caption{Asthma pathway map for the contrast X24IL13-X24}
\label{fig:pathways_single}
\end{figure}

Figure \ref{fig:pathways_single} shows the Asthma pathway map with nodes
coloured based on the gene fold changes in the contrast X24IL13-X24.

Similar reporting capabilities are also provided for the comparative analysis
results of EGSEA. A summary plot that compares two contrasts can be generated as
follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
plotSummary(gsa, gs.label="kegg", contrast=c(1,2), file.name="kegg-summary-cmp")
@

\begin{figure}[!h]
\center
\includegraphics[width=0.6\paperwidth]{{kegg-summary-cmp.dir}.pdf}
\caption{Summary plot for the comparative analysis}
\label{fig:kegg_summary_multi}
\end{figure}

Figure \ref{fig:kegg_summary_multi} shows a comparative summary plot between the
two contrasts of the IL-13 dataset. It clearly highlights the effectiveness of
the IL-13 antagonist in neuteralizing most of the IL-13 stimulated pathways. 

Alternatively, a summary heatmap for all the contrasts at the gene set level can
generated as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>=
plotSummaryHeatmap(gsa, gs.label="kegg", show.vals = "p.adj",
        file.name="il13_sum_heatmap")
@

Figure \ref{fig:kegg_summary_heatmap} shows a summary heatmap for the rankings
of top 20 gene sets of the comparative analysis across all the contrasts. The
EGSEA adjusted p-values are displayed on the heatmap for each gene set. This can
help to identify gene sets that are highly ranked/sgnificant in multiple
contrasts. 

\begin{figure}[!h]
\center
\includegraphics[width=0.6\paperwidth]{il13_sum_heatmap.pdf}
\caption{Summary heatmap for the comparative analysis}
\label{fig:kegg_summary_heatmap}
\end{figure}

To closely see how the antagonist works for a given pathway, a comparative
heatmap can be generated as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
plotHeatmap(gsa, "Asthma", gs.label="kegg", contrast="comparison",
        file.name="asthma_hm_cmp")
@

\begin{figure}[!h]
\center
\includegraphics[width=0.6\paperwidth]{asthma_hm_cmp.pdf}
\caption{Asthma heatmap for the comparative analysis}
\label{fig:heatmaps_multi}
\end{figure}

The heatmap clearly shows that all the genes that were stimulated by IL-13 were
reveresed when the antagonist was introduced (Figure \ref{fig:heatmaps_multi}).
Finally, a comparative pathway map can be used to quickly see which genes of the
Asthma pathway are affected by IL-13 stimulation (Figure
\ref{fig:pathways_multi}) and can be generated as follows

<<echo=TRUE, eval=TRUE,tidy=TRUE,tidy.opts=list(blank=FALSE,width.cutoff=60)>>= 
plotPathway(gsa, "Asthma", gs.label="kegg", contrast=0,  file.name="asthma_pathway_cmp")
@

\begin{figure}[!h]
\center
\includegraphics[width=0.8\paperwidth]{asthma_pathway_cmp.png}
\caption{Asthma pathway map for the comparative analysis}
\label{fig:pathways_multi}
\end{figure}

\section{Ensemble of Gene Set Enrichment Analysis}
Given an RNA-seq dataset $D$ of samples from $N$ experimental conditions, $K$
annotated genes $g_k (k=1,\cdots,K)$, $L$ experimental comparisons of interest
$C_l (l=1, \cdots, L)$, a collection of gene sets $\Gamma$ and $M$ methods for
gene set enrichment analysis, the objective of a GSE analysis is to find the
most relevant gene sets in $\Gamma$ which explain the biological processes
and/or pathways that are perturbed in expression in individual comparisons
and/or across multiple contrasts simultaneously. Numerous statistical gene set
enrichment analysis methods have been proposed in the literature over the past
decade. Each method has its own characteristics and assumptions on the analyzed
dataset and gene sets tested. In principle, gene set tests calculate a
statistic for each gene individually $f(g_k)$ and then integrate these significance scores in a framework to estimate a set significance score $h(\gamma_i)$.

\par We propose seven statistics to combine the individual gene set statistics
across multiple methods, and to rank and hence identify biologically relevant
gene sets. Assume a collection of gene sets $\Gamma$, a given gene set
$\gamma_i \in \Gamma$, and that the GSE analysis results of $M$ methods on
$\gamma_i$ for a specific comparison (represented by ranks $R_i^m$ and
statistical significance scores $p_i^m$, where $m=1, \cdots, M$ and $i=1,
\cdots, |\Gamma|$) are given. The EGSEA scores can then be devised, for each
experimental comparison, as follows:

\begin{itemize}
\item The $p$-value score is the combined $p$-value assigned to $\gamma_i$ and
is calculated using six different methods. 

\item The minimum $p$-value score is the smallest $p$-value calculated for $\gamma_i$

\item The minimum rank score of $\gamma_i$ is the smallest rank assigned to $\gamma_i$

\item The average ranking score is the mean rank across the $M$ ranks

\item The median ranking score is the median rank across the $M$ ranks

\item The majority voting score is the most commonly assigned bin ranking

\item The significance score assigns high scores to the gene sets with strong fold changes and high statistical significance

\end{itemize}

It is worth noting that the $p$-value score can only be calculated under the
independence assumption of individual gene set tests, and thus it is not an
accurate estimate of the ensemble gene set significance, but can still be
useful for ranking results. The significance score is scaled into $[0, 100]$
range for each gene set collection. To learn more about the calculation of each
EGSEA score, the original paper of this work is available at Section 2.


\section{EGSEA report}

\begin{figure}[!t]
\center
\includegraphics[width=0.85\paperwidth]{egsea_report-crop.pdf}
\caption{The main page of the EGSEA HTML report.}
\label{fig:egsea_report}
\end{figure}


Since the number of annotated gene set collections in public databases
continuously increases and there is a growing trend towards generating dynamic
analytical tools, our software tool was developed to enable users to
interactively navigate through the analysis results by generating an HTML
\textit{EGSEA Report} (Figure \ref{fig:egsea_report}). The report presents the results in different ways. For
example, the \textit{Stats table} displays the top $n$ gene sets (where $n$ is
selected by the user) for each experimental comparison and includes all
calculated statistics. Hyperlinks are enabled wherever possible, to access
additional information on the gene sets such as annotation information. 
The gene expression fold changes can be visualized using heat maps for
individual gene sets (Figure \ref{fig:heatmaps} and
\ref{fig:heatmaps_multi}) or projected onto pathway maps where available (e.g.
KEGG gene sets) (Figure \ref{fig:pathways_single} and \ref{fig:pathways_multi}).
The most significant Gene Ontology (GO) terms for each comparison can be viewed
in a GO graph that shows their relationships (Figure \ref{fig:go_terms}).


\par Additionally, EGSEA creates summary plots for each gene set collection to
visualize the overall statistical significance of gene sets (Figure
\ref{fig:kegg_summary} and \ref{fig:kegg_summary_multi}). Two types of summary plots are generated: (i)
a plot that emphasizes the gene regulation direction and the significance score of a gene set and (ii) a plot that emphasizes the set cardinality and its rank.
EGSEA also generates a multidimensional scaling (MDS) plot that shows how
various GSE methods rank a collection of gene sets (Figure \ref{fig:summary_methods}). This plot
gives insights into the similarity of different methods on a given dataset. Finally,
the reporting capabilities of EGSEA can be used to extend any existing or newly
developed GSE method by simply using only that method.


\subsection{Comparative analysis}
Unlike most GSE methods that calculate a gene set enrichment score for a given
gene set under a single experimental contrast (e.g. disease vs. control), the
comparative analysis proposed here allows researchers to estimate the
significance of a gene set across multiple experimental contrasts. This
analysis helps in the identification of biological processes that are perturbed
by multiple experimental conditions simultaneously. Comparative significance
scores are calculated for a gene set.

\par An interesting application of the comparative analysis would be finding
pathways or biological processes that are activated by a stimulation with a
particular cytokine yet are completely inhibited when the cytokine's receptor
is blocked by an antagonist, revealing the functions uniquely associated with
the signaling of that particular receptor as in the experiment below.

\section{EGSEA on a non-human dataset}
Epithelial cells from the mammary glands of female virgin 8-10 week-old mice
were sorted into three populations of basal, luminal progenitor (LP) and mature
luminal (ML) cells. Three independent
samples from each population were profiled via RNA-seq on total RNA using an
Illumina HiSeq 2000 to generate 100bp single-end read libraries. The
\Biocpkg{Rsubread} aligner was used to align these reads to the mouse reference
genome (\textit{mm10}) and mapped reads were summarized into gene-level counts
using \Rfunction{featureCounts}  with default settings. The raw counts are
also normalized using the TMM method. Data are available from the GEO database
as series GSE63310. 

\par To perform EGSEA analysis on this dataset, the following commands can be
invoked in the R console
<<echo=TRUE,  eval=FALSE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
# load the mammary dataset
library(EGSEA)
library(EGSEAdata)
data(mam.data)
v = mam.data$voom
names(v)
v$design
contrasts = mam.data$contra
contrasts
# build the gene set collections 
gs.annots = buildIdx(entrezIDs=rownames(v$E), species="mouse",
        msigdb.gsets = "c2",
        kegg.exclude = "all")
names(gs.annots)
# create Entrez IDs - Symbols map
symbolsMap = v$genes[,c(1,3)]
colnames(symbolsMap) = c("FeatureID", "Symbols")
symbolsMap[, "Symbols"] = as.character(symbolsMap[, "Symbols"])
# replace NA Symbols with IDs
na.sym = is.na(symbolsMap[, "Symbols"])
na.sym
symbolsMap[na.sym, "Symbols"] = symbolsMap[na.sym, "FeatureID"]
# perform the EGSEA analysis
# set report = TRUE to generate the EGSEA interactive report
baseMethods = c("camera", "safe", "gage", "padog", "zscore",
        "gsva", "globaltest", "ora")
gsa = egsea(voom.results=v, contrasts=contrasts, gs.annots=gs.annots, 
        symbolsMap=symbolsMap, baseGSEAs=baseMethods, 
        sort.by="med.rank", 
        num.threads=4, report=FALSE)	
# show top 20 comparative gene sets in C2 collection
summary(gsa)
topSets(gsa, gs.label="c2", contrast="comparison", number = 20)
@

\section{EGSEA on a count matrix}
The EGSEA analysis can be also performed on the count matrix directly without
the need of having a \Robject{voom} object in advance. The \Rfunction{egsea.cnt}
can be invoked on a count matrix given the group of each sample is provided with
design and contrast matrices as it is illustrated in this example. This
function uses the \Rfunction{voom} function from the \Biocpkg{limma}
pakcage to convert the RNA-seq counts into expression values.

\par Here, the IL-13 human dataset is reanalyzed using the count matrix.

<<echo=TRUE,  eval=FALSE,tidy=TRUE,tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
# load the count matrix and other relevant data
library(EGSEAdata)
data(il13.data.cnt)
cnt = il13.data.cnt$counts
group = il13.data.cnt$group
group
design = il13.data.cnt$design
contrasts = il13.data.cnt$contra
genes = il13.data.cnt$genes
# build the gene set collections
gs.annots = buildIdx(entrezIDs=rownames(cnt), species="human", msigdb.gsets="none",
 			 kegg.exclude = c("Metabolism"))
# perform the EGSEA analysis
# set report = TRUE to generate the EGSEA interactive report
gsa = egsea.cnt(counts=cnt, group=group, design=design, contrasts=contrasts,  
        gs.annots=gs.annots, symbolsMap=genes, baseGSEAs=egsea.base()[-c(2,12)], 
 	    sort.by="avg.rank", num.threads = 4, report=FALSE)
@

\section{EGSEA on a list of genes}
Since performing simple over-representation analysis on large collections of
gene sets is not readily available in Bioconductor, an ORA analysis was
augmented to the \Biocpkg{EGSEA} package so that all the reporting capabilities
of EGSEA are enabled. 

\par To perform ORA using the DE genes of the \textit{X24IL13-X24} contrast
from the IL-13 dataset, cut-off thresholds of p-value=0.05 and logFC = 1 are
used to select a subset of DE genes. Then, the \Rfunction{egsea.ora} function is invoked as it is
illulstrated in the following example

<<echo=TRUE, eval=TRUE, tidy=TRUE, tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
# load IL-13 dataset
library(EGSEAdata)
data(il13.data)
voom.results = il13.data$voom
contrast = il13.data$contra
# find Differentially Expressed genes
library(limma)
vfit = lmFit(voom.results, voom.results$design)
vfit = contrasts.fit(vfit, contrast)
vfit = eBayes(vfit)
# select DE genes (Entrez IDs and logFC) at p-value <= 0.05 and |logFC| >= 1
top.Table = topTable(vfit, coef=1, number=Inf, p.value=0.05, lfc=1)
deGenes = as.character(top.Table$FeatureID)
logFC = top.Table$logFC
names(logFC) = deGenes
# build the gene set collection index 
gs.annots = buildIdx(entrezIDs=deGenes, species="human", msigdb.gsets="none",
 			kegg.exclude = c("Metabolism"))
# perform the ORA analysis 
# set report = TRUE to generate the EGSEA interactive report
gsa = egsea.ora(entrezIDs=deGenes, universe= as.character(voom.results$genes[,1]),
				logFC =logFC, title="X24IL13-X24",  gs.annots=gs.annots, 
  			    symbolsMap=top.Table[, c(1,2)], display.top = 5,          
  			    egsea.dir="./il13-egsea-ora-report", num.threads = 4, report=FALSE)

@

\section{Non-standard gene set collections}
Scientists usually have their own lists of gene sets and are interested in
finding which sets are significant in the investigated dataset. Additional
collections of gene sets can be easily added and tested using the EGSEA
algorithm. The \Rfunction{buildCustomIdx} function indexes newly created
gene sets and attach gene set annotation if provided. To illustrate the use of
this function, assume a list of gene sets is available where each gene set is
represented by a character vector of Entrez Gene IDs. In this example, 50 gene
sets were selected from the KEGG collection and then they were used to build a
custom gene set collection index.

<<echo=TRUE, eval=TRUE, tidy=TRUE, tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
library(EGSEAdata)
data(il13.data)
v = il13.data$voom
# load KEGG pathways
data(kegg.pathways)
# select 50 pathways
gsets = kegg.pathways$human$kg.sets[1:50]
gsets[1]
# build custom gene set collection using these 50 pathways
gs.annot = buildCustomIdx(entrezIDs=rownames(v$E), gsets= gsets, species="human")
class(gs.annot)
show(gs.annot)
@

The \Rfunction{buildCustomIdx} creates an annotation data frame for the gene
set collection if the \textit{anno} parameter is not provided. Once the gene set
collection is indexed, it can be used with any of the \Biocpkg{EGSEA} functions:
\Rfunction{egsea}, \Rfunction{egsea.cnt} or \Rfunction{egsea.ora}.


\section{Adding new GSE method}
If you have an interesting gene set test method that you would like to add to
the EGSEA framework, please contact us and we will be happy to add your method
to the next release of \Biocpkg{EGSEA}. We do not allow users to add new methods
by themselves because this procedure is a straightforward and is a
method-dependent. 

\section{Packages used}
<<echo=TRUE, eval=TRUE, tidy=TRUE, tidy.opts=list(blank=FALSE, width.cutoff=60)>>=
sessionInfo()
@

\addcontentsline{toc}{section}{References}
\bibliography{references}

\end{document}


% R CMD Sweave --engine=knitr::knitr --pdf EGSEA.Rnw