STATUS_TABLE.tex

%& -shell-escape
\documentclass[11pt]{article}

\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{lmodern}

%\usepackage[latin1]{inputenc}
\usepackage[english]{babel}
\usepackage[paperwidth=18cm, paperheight=10cm,margin=0.5cm]{geometry}
\usepackage{helvet}
\usepackage{times}
%\usepackage{subfigure}
\usepackage{enumitem}

%\usepackage{unnumberedcaption}
\usepackage{multirow}
\usepackage{graphics,graphicx,epsfig,rotating}
\usepackage{amsfonts,amsmath,supertabular,tabularx,amstext}
\usepackage[table]{xcolor}
\usepackage{color}
\usepackage{verbatim}
\usepackage{stmaryrd} 
\usepackage{array}
\usepackage{subfig}
%\usepackage[noae]{Sweave}

\usepackage{longtable}
\usepackage{threeparttable}

\usepackage[]{natbib}
\bibpunct{(}{)}{;}{author-year}{}{,} 

\RequirePackage{fancyvrb}
\RequirePackage{listings}

\usepackage{hyperref}
\usepackage[right]{lineno}

\rmfamily

\definecolor{lightgray}{rgb}{0.75,0.75,0.75}

%\oddsidemargin 0cm
%\evensidemargin 0cm
%%\textwidth 17.2cm
%\topmargin 0cm
%\textheight 10.2cm
%\textwidth 18cm
%\marginparsep 0pt
\renewcommand{\baselinestretch}{1} 
%color

\usepackage{titlesec}
\titleformat{\section}{\Large\bfseries}{}{0pt}{}
\titleformat{\subsection}{\Large\itshape}{}{0pt}{}




\begin{document}
\definecolor{red2}{rgb}{1,0.5,0.5}
\definecolor{lightred}{rgb}{1,0.8,0.8}

\definecolor{lightblue}{rgb}{0,0.60,0.86}

\definecolor{redblue}{rgb}{0.3,0.7,0.43}

\definecolor{darkgreen}{rgb}{0.1,0.6,0.1}
\definecolor{Lightgray}{rgb}{0.95,0.95,0.95}
\definecolor{lightgray}{rgb}{0.75,0.75,0.75}
\definecolor{darkgray}{rgb}{0.35,0.35,0.35}
\definecolor{darkgray2}{rgb}{0.90,0.90,0.90}
\definecolor{darkred}{rgb}{0.6,0.1,0.1}

%\begin{titlepage}




\setcounter{page}{1}

%\tableofcontents
%\newpage


%\newpage
%%%%%%%%%%%%%%%%%  citations %%%%%%%%%%%%%%%%%%%
\setcounter{equation}{0}
\setcounter{figure}{0}
\setcounter{section}{0}
\renewcommand{\thefigure}{S\arabic{figure}}
\renewcommand{\thetable}{S\arabic{table}}
\renewcommand{\theequation}{S\arabic{equation}}

%\newpage


\begin{footnotesize}
\begin{threeparttable}
\begin{tabular}[htp!]{m{1.4cm} m{1.7cm} m{1.4cm} m{1.7cm} m{4.5cm} m{1.4cm} m{1.4cm}}
\caption{\textbf{Table of variant STATUS and GT (genotype), as a function of variant detection and the power to detect variants in matched normal and tumor samples.}}\\
\hline
\textbf{Variant in Normal} & \textbf{Power to detect variant in Normal} & \textbf{Variant in Tumor} & \textbf{Power to detect variant in Tumor} & \textbf{STATUS} & \textbf{Normal GT} & \textbf{Tumor GT}\\
\hline
\rowcolor{lightgray}no & no & no& no& . & ./. & ./. \tnote{*}\\
no & no & no& \textbf{YES}& . & ./. & 0/0 \tnote{*}\\
\rowcolor{lightgray}no & no & \textbf{YES}& \textbf{YES} or no  & UNKNOWN & ./. & 0/1 or 1/1 \\
no & \textbf{YES} & no& no& . & 0/0 & ./. \tnote{*}\\
\rowcolor{lightgray}no & \textbf{YES} & no& \textbf{YES}& . & 0/0 & 0/0 \tnote{*}\\
no & \textbf{YES} & \textbf{YES}& \textbf{YES} or no & SOMATIC \tnote{\textdagger} & 0/0 & 0/1 or 1/1 \\
\rowcolor{lightgray}\textbf{YES} & \textbf{YES} or no & no& no& GERMLINE\_UNCONFIRMABLE & 0/1 or 1/1 & ./. \\
\textbf{YES} & \textbf{YES} or no & no& \textbf{YES}& GERMLINE\_UNCONFIRMED & 0/1 or 1/1 & 0/0 \\
\rowcolor{lightgray}\textbf{YES} & \textbf{YES} or no & \textbf{YES}& \textbf{YES} or no & GERMLINE\_CONFIRMED & 0/1 or 1/1 & 0/1 or 1/1\\
\hline
\label{tab:sumstats}
\end{tabular}
\begin{tablenotes}
\item[*] power is computed using a binomial distribution with mean $power\_min\_af$ (default value is 0.01)
\item[\textdagger] only in Tumor; Normal STATUS is ``."
\end{tablenotes}

\end{threeparttable}

\end{footnotesize}



\end{document}