build based on 44d88d5

dev/index.html

@@ -1236,4 +1236,4 @@
 PVALFILE=/user/dir/pvalfiles/sbp.test.diabetes.chr${CHR}.${CHUNKIDX}of${NCHUNKS}.txt
 
 module load julia
-time julia --project=${PROJECTDIR} ${PROJECTDIR}/scoretest_bp.jl ${BGENDIR} ${CHR} ${FITTED_NULL} ${PVALFILE} ${CHUNKIDX} ${NCHUNKS}</code></pre><p>and this could be submitted using the <code>qsub</code> command.</p><h2 id="Troubleshooting"><a class="docs-heading-anchor" href="#Troubleshooting">Troubleshooting</a><a id="Troubleshooting-1"></a><a class="docs-heading-anchor-permalink" href="#Troubleshooting" title="Permalink"></a></h2><p>If there are issues you&#39;re encountering with running TrajGWAS, the following are possible remedies.</p><ul><li>Null Model<ul><li>Issues with null model convergence may be solved by choosing alternate starting values for parameters, using a different solver, transforming variables, and increasing the number of runs (WiSER runs). These are detailed in the <a href="https://github.com/OpenMendel/WiSER.jl/blob/master/docs/src/model_fitting.md#tips-for-improving-estimation">WiSER documentation here</a>. <code>init = x -&gt; WiSER.init_ls!(x; gniters=0)</code> works fine in general. </li></ul></li><li>GWAS Results<ul><li>If you use the score test instead of the SPA-score test (SPA is default for single-SNP analyses), then there can be inflation in type I error and decreased power when (a) the sample size is small, (b) the number of repeated measures is low, or (c) the variants analyzed are rare with low minor allele frequencies. In these cases, the score test is not optimal and it is suggested to use the SPA version (<code>usespa=true</code>). SPA is only implemented for single-SNP analyses. These issues can occur in both Wald and score tests. </li></ul></li></ul><p>If you notice any problems with your output or results, <a href="https://github.com/OpenMendel/TrajGWAS.jl/issues">file an issue</a>. </p></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 18 December 2024 02:35">Wednesday 18 December 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+time julia --project=${PROJECTDIR} ${PROJECTDIR}/scoretest_bp.jl ${BGENDIR} ${CHR} ${FITTED_NULL} ${PVALFILE} ${CHUNKIDX} ${NCHUNKS}</code></pre><p>and this could be submitted using the <code>qsub</code> command.</p><h2 id="Troubleshooting"><a class="docs-heading-anchor" href="#Troubleshooting">Troubleshooting</a><a id="Troubleshooting-1"></a><a class="docs-heading-anchor-permalink" href="#Troubleshooting" title="Permalink"></a></h2><p>If there are issues you&#39;re encountering with running TrajGWAS, the following are possible remedies.</p><ul><li>Null Model<ul><li>Issues with null model convergence may be solved by choosing alternate starting values for parameters, using a different solver, transforming variables, and increasing the number of runs (WiSER runs). These are detailed in the <a href="https://github.com/OpenMendel/WiSER.jl/blob/master/docs/src/model_fitting.md#tips-for-improving-estimation">WiSER documentation here</a>. <code>init = x -&gt; WiSER.init_ls!(x; gniters=0)</code> works fine in general. </li></ul></li><li>GWAS Results<ul><li>If you use the score test instead of the SPA-score test (SPA is default for single-SNP analyses), then there can be inflation in type I error and decreased power when (a) the sample size is small, (b) the number of repeated measures is low, or (c) the variants analyzed are rare with low minor allele frequencies. In these cases, the score test is not optimal and it is suggested to use the SPA version (<code>usespa=true</code>). SPA is only implemented for single-SNP analyses. These issues can occur in both Wald and score tests. </li></ul></li></ul><p>If you notice any problems with your output or results, <a href="https://github.com/OpenMendel/TrajGWAS.jl/issues">file an issue</a>. </p></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Thursday 19 December 2024 02:35">Thursday 19 December 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/search/index.html

@@ -1,2 +1,2 @@
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