Built site for gh-pages

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@@ -1 +1 @@
-b5d8cf0d
+7cb7ad32

search.json

@@ -81,6 +81,6 @@
     "href": "simulation-analysis.html",
     "title": "Simulation analysis",
     "section": "",
-    "text": "renv::load(here::here())\n\n- The project is out-of-sync -- use `renv::status()` for details.\n\nlibrary(dplyr)\nlibrary(readr)\nlibrary(ggplot2)\nlibrary(glue)\n\n\nlocus <- c(\"PTPN22\", \"IL21\", \"IRF5\")\nsimulation_data <- lapply(locus, function(x) {\n  here::here(glue(\"output/data/sim-result-{x}.rds\")) |>\n  read_rds() |>\n  mutate(locus = x)\n}) |>\n  bind_rows()\n\n\nsimulation_data |>\n  mutate(\n    fp = hyp == \"h3\" & pp_h4 >= 0.8,\n    tp = hyp == \"h4\" & pp_h4 >= 0.8,\n    fn = hyp == \"h4\" & pp_h4 < 0.8\n  ) |>\n  summarise(\n    n_tp = sum(tp),\n    n_fn = sum(fn), \n    n_fp = sum(fp),\n    .by = prior\n  ) |>\n  mutate(\n    recall = n_tp / (n_tp + n_fn),\n    precision = n_tp / (n_tp + n_fp)\n  )\n\n# A tibble: 2 × 6\n  prior     n_tp  n_fn  n_fp recall precision\n  <chr>    <int> <int> <int>  <dbl>     <dbl>\n1 unif       125    25    14  0.833     0.899\n2 non_unif   124    26    12  0.827     0.912\n\n\n\nsimulation_data |>\n  ggplot(aes(hyp, pp_h4, fill = prior)) + \n  geom_boxplot(position = \"dodge\") + \n  geom_hline(yintercept = 0.8, linetype = \"dashed\") +\n  theme_bw() + \n  labs(\n    x = \"True hypothesis\", \n    y = \"Mean Pr(H4)\",\n    fill = \"Prior type\"\n  )\n\n\n\n\n\nsimulation_data |>\n  ggplot(aes(hyp, pp_h4, fill = prior)) +\n  geom_boxplot(position = \"dodge\") +\n  geom_hline(yintercept = 0.8, linetype = \"dashed\") +\n  theme_bw() +\n  labs(\n    x = \"True hypothesis\",\n    y = \"Mean Pr(H4)\",\n    fill = \"Prior type\"\n  ) +\n  facet_wrap(~locus)"
+    "text": "renv::load(here::here())\n\n- The project is out-of-sync -- use `renv::status()` for details.\n\nlibrary(dplyr)\nlibrary(readr)\nlibrary(ggplot2)\nlibrary(glue)\n\ndevtools::load_all(\"~/coloc\")\n\n\nlocus <- c(\"PTPN22\", \"IL21\", \"IRF5\", \"IFT172\")\nsimulation_data <- lapply(locus, function(x) {\n  here::here(glue(\"output/data/sim-result-{x}.rds\")) |>\n  read_rds() |>\n  mutate(locus = x)\n}) |>\n  bind_rows()\n\n\nsimulation_data |>\n  mutate(\n    fp = hyp == \"h3\" & pp_h4 >= 0.8,\n    tp = hyp == \"h4\" & pp_h4 >= 0.8,\n    fn = hyp == \"h4\" & pp_h4 < 0.8\n  ) |>\n  summarise(\n    n_tp = sum(tp),\n    n_fn = sum(fn), \n    n_fp = sum(fp),\n    .by = prior\n  ) |>\n  mutate(\n    recall = n_tp / (n_tp + n_fn),\n    precision = n_tp / (n_tp + n_fp)\n  )\n\n# A tibble: 2 × 6\n  prior     n_tp  n_fn  n_fp recall precision\n  <chr>    <int> <int> <int>  <dbl>     <dbl>\n1 unif       132    67     9  0.663     0.936\n2 non_unif   141    58    10  0.709     0.934\n\n\n\nsimulation_data |>\n  ggplot(aes(hyp, pp_h4, fill = prior)) + \n  geom_boxplot(position = \"dodge\") + \n  geom_hline(yintercept = 0.8, linetype = \"dashed\") +\n  theme_bw() + \n  labs(\n    x = \"True hypothesis\", \n    y = \"Mean Pr(H4)\",\n    fill = \"Prior type\"\n  )\n\n\n\n\n\nsimulation_data |>\n  ggplot(aes(hyp, pp_h4, fill = prior)) +\n  geom_boxplot(position = \"dodge\") +\n  geom_hline(yintercept = 0.8, linetype = \"dashed\") +\n  theme_bw() +\n  labs(\n    x = \"True hypothesis\",\n    y = \"Mean Pr(H4)\",\n    fill = \"Prior type\"\n  ) +\n  facet_wrap(~locus)\n\n\n\n\n\nloci <- c(\"PTPN22\", \"IL21\", \"IRF5\", \"IFT172\")\nprior_weights <- list()\npos <- list()\nlocus <- list()\nfor (i in seq_along(loci)) {\n  file <- glue(here::here(\"data/{loci[[i]]}.vcf.gz.impute.legend\"))\n  legend <- read_delim(file, show_col_types = FALSE) \n  pos[[i]] <- legend$pos\n  prior_weights[[i]] <- compute_eqtl_tss_dist_prior_weights(\n    pos[[i]],\n    round(median(pos[[i]]), 0),\n    read_rds(here::here(\"output/densities/eqtlgen.rds\"))\n  )\n  locus[[i]] <- rep(loci[[i]], length(pos[[i]]))\n}\n\ntibble(\n  locus = unlist(locus),\n  pos = unlist(pos),\n  prior_weight = unlist(prior_weights)\n) |> \n  ggplot(aes(pos, prior_weight)) + \n  geom_point() + \n  facet_wrap(~ locus, scales = \"free_x\") + \n  labs(\n    x = \"Position\",\n    y = \"Prior weight\"\n  ) + \n  theme_bw()"
   }
 ]

simulation-analysis.html

@@ -160,10 +160,12 @@ <h1 class="title">Simulation analysis</h1>
 <div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span>
 <span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(readr)</span>
 <span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
-<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(glue)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(glue)</span>
+<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">load_all</span>(<span class="st">"~/coloc"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <div class="cell">
-<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>locus <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">"PTPN22"</span>, <span class="st">"IL21"</span>, <span class="st">"IRF5"</span>)</span>
+<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>locus <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">"PTPN22"</span>, <span class="st">"IL21"</span>, <span class="st">"IRF5"</span>, <span class="st">"IFT172"</span>)</span>
 <span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>simulation_data <span class="ot">&lt;-</span> <span class="fu">lapply</span>(locus, <span class="cf">function</span>(x) {</span>
 <span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>  here<span class="sc">::</span><span class="fu">here</span>(<span class="fu">glue</span>(<span class="st">"output/data/sim-result-{x}.rds"</span>)) <span class="sc">|&gt;</span></span>
 <span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a>  <span class="fu">read_rds</span>() <span class="sc">|&gt;</span></span>
@@ -192,8 +194,8 @@ <h1 class="title">Simulation analysis</h1>
 <pre><code># A tibble: 2 × 6
   prior     n_tp  n_fn  n_fp recall precision
   &lt;chr&gt;    &lt;int&gt; &lt;int&gt; &lt;int&gt;  &lt;dbl&gt;     &lt;dbl&gt;
-1 unif       125    25    14  0.833     0.899
-2 non_unif   124    26    12  0.827     0.912</code></pre>
+1 unif       132    67     9  0.663     0.936
+2 non_unif   141    58    10  0.709     0.934</code></pre>
 </div>
 </div>
 <div class="cell">
@@ -227,6 +229,40 @@ <h1 class="title">Simulation analysis</h1>
 <p><img src="simulation-analysis_files/figure-html/unnamed-chunk-4-1.png" class="img-fluid" width="672"></p>
 </div>
 </div>
+<div class="cell">
+<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>loci <span class="ot">&lt;-</span> <span class="fu">c</span>(<span class="st">"PTPN22"</span>, <span class="st">"IL21"</span>, <span class="st">"IRF5"</span>, <span class="st">"IFT172"</span>)</span>
+<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a>prior_weights <span class="ot">&lt;-</span> <span class="fu">list</span>()</span>
+<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a>pos <span class="ot">&lt;-</span> <span class="fu">list</span>()</span>
+<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a>locus <span class="ot">&lt;-</span> <span class="fu">list</span>()</span>
+<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (i <span class="cf">in</span> <span class="fu">seq_along</span>(loci)) {</span>
+<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a>  file <span class="ot">&lt;-</span> <span class="fu">glue</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"data/{loci[[i]]}.vcf.gz.impute.legend"</span>))</span>
+<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a>  legend <span class="ot">&lt;-</span> <span class="fu">read_delim</span>(file, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>) </span>
+<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a>  pos[[i]] <span class="ot">&lt;-</span> legend<span class="sc">$</span>pos</span>
+<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a>  prior_weights[[i]] <span class="ot">&lt;-</span> <span class="fu">compute_eqtl_tss_dist_prior_weights</span>(</span>
+<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a>    pos[[i]],</span>
+<span id="cb9-11"><a href="#cb9-11" aria-hidden="true" tabindex="-1"></a>    <span class="fu">round</span>(<span class="fu">median</span>(pos[[i]]), <span class="dv">0</span>),</span>
+<span id="cb9-12"><a href="#cb9-12" aria-hidden="true" tabindex="-1"></a>    <span class="fu">read_rds</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"output/densities/eqtlgen.rds"</span>))</span>
+<span id="cb9-13"><a href="#cb9-13" aria-hidden="true" tabindex="-1"></a>  )</span>
+<span id="cb9-14"><a href="#cb9-14" aria-hidden="true" tabindex="-1"></a>  locus[[i]] <span class="ot">&lt;-</span> <span class="fu">rep</span>(loci[[i]], <span class="fu">length</span>(pos[[i]]))</span>
+<span id="cb9-15"><a href="#cb9-15" aria-hidden="true" tabindex="-1"></a>}</span>
+<span id="cb9-16"><a href="#cb9-16" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb9-17"><a href="#cb9-17" aria-hidden="true" tabindex="-1"></a><span class="fu">tibble</span>(</span>
+<span id="cb9-18"><a href="#cb9-18" aria-hidden="true" tabindex="-1"></a>  <span class="at">locus =</span> <span class="fu">unlist</span>(locus),</span>
+<span id="cb9-19"><a href="#cb9-19" aria-hidden="true" tabindex="-1"></a>  <span class="at">pos =</span> <span class="fu">unlist</span>(pos),</span>
+<span id="cb9-20"><a href="#cb9-20" aria-hidden="true" tabindex="-1"></a>  <span class="at">prior_weight =</span> <span class="fu">unlist</span>(prior_weights)</span>
+<span id="cb9-21"><a href="#cb9-21" aria-hidden="true" tabindex="-1"></a>) <span class="sc">|&gt;</span> </span>
+<span id="cb9-22"><a href="#cb9-22" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(pos, prior_weight)) <span class="sc">+</span> </span>
+<span id="cb9-23"><a href="#cb9-23" aria-hidden="true" tabindex="-1"></a>  <span class="fu">geom_point</span>() <span class="sc">+</span> </span>
+<span id="cb9-24"><a href="#cb9-24" aria-hidden="true" tabindex="-1"></a>  <span class="fu">facet_wrap</span>(<span class="sc">~</span> locus, <span class="at">scales =</span> <span class="st">"free_x"</span>) <span class="sc">+</span> </span>
+<span id="cb9-25"><a href="#cb9-25" aria-hidden="true" tabindex="-1"></a>  <span class="fu">labs</span>(</span>
+<span id="cb9-26"><a href="#cb9-26" aria-hidden="true" tabindex="-1"></a>    <span class="at">x =</span> <span class="st">"Position"</span>,</span>
+<span id="cb9-27"><a href="#cb9-27" aria-hidden="true" tabindex="-1"></a>    <span class="at">y =</span> <span class="st">"Prior weight"</span></span>
+<span id="cb9-28"><a href="#cb9-28" aria-hidden="true" tabindex="-1"></a>  ) <span class="sc">+</span> </span>
+<span id="cb9-29"><a href="#cb9-29" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme_bw</span>() </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="cell-output-display">
+<p><img src="simulation-analysis_files/figure-html/unnamed-chunk-5-1.png" class="img-fluid" width="672"></p>
+</div>
+</div>
 
 
 

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