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\begin{table}[htdp]  \caption{Description of mathematical variables used in the combined haplotype test}  \begin{center}  \small  \begin{tabular}{ l l }  % \hline \hline  % Variable & Description\\  \hline  \multicolumn{2}{l}{\textbf{Index variables}}\\  $h$ & test number (one per test SNP / target region pair) \\  $i$ & individual\\  $j$ & target region\\  $k$ & SNP within target region\\  $m$ & test SNP\\  \multicolumn{2}{l}{\textbf{Latent variables}}\\  $\alpha_h$ & molecular phenotype level of the reference allele for test $h$\\  $\beta_h$ & molecular phenotype level of the alternative allele for test $h$\\  $p_h$ & fraction of allele-specific reads expected from reference allele ($p_h = \frac{\alpha_h}{\alpha_h + \beta_h}$)\\  $T^{*}_{i,j}$ & genotype-independent expected total read count for individual $i$, target region $j$\\  $\lambda_{hi}$ & expected total read count for test $h$, individual $i$\\  $\Phi_i$ & overdispersion of read counts for individual $i$ (across all tests)\\  $\eta_j$ & overdispersion of read counts for test number $j$ (across all individuals)\\  $\Upsilon_i$ & overdispersion of allele-specific reads for individual $i$\\  \multicolumn{2}{l}{\textbf{Observed variables}}\\  $x_{ij}$ & number of reads for individual $i$, target region $j$\\  $G_{im}$ & genotype call for individual $i$, test SNP $m$\\   $T_{i}$ & total number of genome-wide mapped reads for individual $i$\\  $n_{ik}$ & total number of allele-specific reads for individual $i$, target SNP $k$\\  $y_{ik}$ & number of allele-specific reads from reference haplotype for individual $i$, target SNP $k$\\  $H_{ik}$ & probability individual $i$ is heterozygous for target SNP $k$\\  \hline \hline  \end{tabular}  \end{center}  \label{tab:readcounts}  \end{table}%