deletions | additions       diff --git a/Table of variables.tex b/Table of variables.tex  deleted file mode 100644  index cd9c3bd..0000000  --- a/Table of variables.tex  +++ /dev/null 
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\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}  diff --git a/layout.md b/layout.md  index 96f6ff1..b1d8221 100644  --- a/layout.md  +++ b/layout.md 
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untitled.tex  QTL testing with WASP.tex  CHT intro.tex  Table of variables.tex  Basic Model.tex  Modeling read depths.tex  Correcting read depth and GC.tex