topGO.Rnw

% -*- mode: noweb; noweb-default-code-mode: R-mode; -*-
\documentclass{article}

\usepackage{geometry}
\geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm}

%headers and footers
\usepackage{fancyhdr}
\setlength{\headheight}{15pt}
\pagestyle{fancyplain}
\lhead{\fancyplain{}{\thepage}}
\chead{}
\rhead{\fancyplain{}{\bfseries Ant1-KO TopGO Analysis}}
\cfoot{}
\lfoot{\includegraphics[width=0.1\textwidth]{/nas/is1/leipzig/ganguly/src/R/bicLogo.png}\\[1cm]}


%hyperlink setup
\usepackage{hyperref}
\usepackage{xcolor}
\definecolor{dark-red}{rgb}{0.4,0.15,0.15}
\definecolor{dark-blue}{rgb}{0.15,0.15,0.4}
\definecolor{medium-blue}{rgb}{0,0,0.5}
\hypersetup{
    colorlinks, linkcolor={dark-red},
    citecolor={dark-blue}, urlcolor={medium-blue}
}


\usepackage{longtable}
\usepackage{rotating}

%underscores in variable names cause problems
%\usepackage{underscore}

\begin{document}
\SweaveOpts{concordance=TRUE}
\title{Ant1-KO TopGO Analysis}
\author{Jeremy Leipzig}
\maketitle
\tableofcontents
\pagebreak
<<setup,echo=FALSE,results=hide>>=
library(topGO)
library(org.Mm.eg.db)
library(xtable)
@

\section{Introduction}
TopGO \cite{Alexa} provides additional tools for exploring GO enrichment.

The classicFisher is a filtered list approach - enrichment is strictly based on counts of genes associated with the GO terms.

Kolmogorov-Smirnov test is supposed to use differential p-values to weight enrichment. The elim method was design to be more conservative then the classic method.

The "Significant" column is not relevant to the most up and down regulated tables - since those rely on running TopGO using the fold change metric instead of p.val.

<<topgo,results=hide,echo=F>>=
muscleGos<-get(load("muscleGO.RData"))
heartGos<-get(load("heartGO.RData"))
ont<-'BP'
@
\section{Muscle}
<<musclego,echo=FALSE,results=tex>>=
for(crit in c('de','hot','cold')){
  print(muscleGos[[crit]][[ont]]$xtable,include.rownames=FALSE, tabular.environment = "longtable", floating = FALSE, size="\\scriptsize")
}
@
\pagebreak
<<musclecc,echo=FALSE,results=tex>>=
ont<-'CC'
<<musclego>>
@
\pagebreak
<<musclemf,echo=FALSE,results=tex>>=
ont<-'MF'
<<musclego>>
@
\pagebreak
\section{Heart}
<<heartsetup,echo=FALSE,results=hide>>=
ont<-'BP'
@

<<heartgo,echo=FALSE,results=tex>>=
for(crit in c('de','hot','cold')){
  print(heartGos[[crit]][[ont]]$xtable,include.rownames=FALSE, tabular.environment = "longtable", floating = FALSE, size="\\scriptsize")
}
@
\pagebreak
<<heartcc,echo=FALSE,results=tex>>=
ont<-'CC'
<<heartgo>>
@
\pagebreak
<<heartmf,echo=FALSE,results=tex>>=
ont<-'MF'
<<heartgo>>
@

\pagebreak
The R session information (including the OS info, R version and all
packages used):

<<session-info,echo=FALSE,results=tex>>=
toLatex(sessionInfo())

@

<<git,echo=FALSE,results=hide>>=
commit<-system("git rev-parse --verify HEAD",intern=TRUE)
time<-Sys.time()
@
\rfoot{$ \Sexpr{commit} \Sexpr{time} $}

\begin{thebibliography}{100}  % start the bibliography

\small  			% put the bibliography in a small font


\bibitem{Alexa} Alexa, A., Rahnenfuhrer, J., and Lengauer, T. (2006).
Improved scoring of functional groups from gene expression data by decorrelating 
go graph structure. Bioinformatics (Oxford, England), 22:1600-1607.
10.1093/bioinformatics/btl140.
\end{thebibliography}  	% end the bibliography


\end{document}