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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.0.36">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<title>IMPACT Example Script</title>
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<script src="impact-example-script_files/libs/bootstrap/bootstrap.min.js"></script>
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<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc">
<h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#pulling-data" id="toc-pulling-data" class="nav-link active" data-scroll-target="#pulling-data">Pulling Data</a></li>
<li><a href="#processing-data" id="toc-processing-data" class="nav-link" data-scroll-target="#processing-data">Processing Data</a>
<ul class="collapse">
<li><a href="#check-mutation-status" id="toc-check-mutation-status" class="nav-link" data-scroll-target="#check-mutation-status">Check Mutation Status</a></li>
<li><a href="#zero-alteration-patients" id="toc-zero-alteration-patients" class="nav-link" data-scroll-target="#zero-alteration-patients">Zero Alteration Patients</a></li>
<li><a href="#create-gene-binary-matrix" id="toc-create-gene-binary-matrix" class="nav-link" data-scroll-target="#create-gene-binary-matrix">Create Gene Binary Matrix</a></li>
<li><a href="#confirm-zero-patients-are-included-in-binary-matrix" id="toc-confirm-zero-patients-are-included-in-binary-matrix" class="nav-link" data-scroll-target="#confirm-zero-patients-are-included-in-binary-matrix">Confirm Zero Patients Are Included in Binary Matrix</a></li>
<li><a href="#annotate-nas-in-impact-panels" id="toc-annotate-nas-in-impact-panels" class="nav-link" data-scroll-target="#annotate-nas-in-impact-panels">Annotate NAs in IMPACT Panels</a>
<ul class="collapse">
<li><a href="#recode-aliases" id="toc-recode-aliases" class="nav-link" data-scroll-target="#recode-aliases">Recode Aliases</a></li>
</ul></li>
</ul></li>
<li><a href="#analyzing-data" id="toc-analyzing-data" class="nav-link" data-scroll-target="#analyzing-data">Analyzing Data</a></li>
<li><a href="#visualizing-data" id="toc-visualizing-data" class="nav-link" data-scroll-target="#visualizing-data">Visualizing Data</a>
<ul class="collapse">
<li><a href="#get-tmb" id="toc-get-tmb" class="nav-link" data-scroll-target="#get-tmb">Get TMB</a></li>
</ul></li>
</ul>
</nav>
</div>
<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">IMPACT Example Script</h1>
</div>
<div class="quarto-title-meta">
</div>
</header>
<section id="pulling-data" class="level1">
<h1>Pulling Data</h1>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(cbioportalR)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.3.6 ✔ purrr 0.3.4
✔ tibble 3.1.8 ✔ dplyr 1.0.10
✔ tidyr 1.2.0 ✔ stringr 1.4.1
✔ readr 2.1.2 ✔ forcats 0.5.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()</code></pre>
</div>
<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="co">#devtools::install_github("MSKCC-Epi-Bio/gnomeR")</span></span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(gnomeR)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Attaching package: 'gnomeR'
The following object is masked from 'package:cbioportalR':
impact_gene_info</code></pre>
</div>
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(gtsummary)</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="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="fu">set_cbioportal_db</span>(<span class="st">"public"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>✔ You are successfully connected!</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>✔ base_url for this R session is now set to "www.cbioportal.org/api" </code></pre>
</div>
<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><span class="fu">test_cbioportal_db</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>✔ You are successfully connected!</code></pre>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>all_studies <span class="ot"><-</span> <span class="fu">available_studies</span>()</span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a>all_studies <span class="sc">%>%</span> <span class="fu">head</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 6 × 13
studyId name descr…¹ publi…² groups status impor…³ allSa…⁴ readP…⁵ cance…⁶
<chr> <chr> <chr> <lgl> <chr> <int> <chr> <int> <lgl> <chr>
1 acc_tcga Adre… "TCGA … TRUE PUBLIC 0 2022-0… 92 TRUE acc
2 bcc_unige… Basa… "Whole… TRUE PUBLIC 0 2022-0… 293 TRUE bcc
3 ampca_bcm… Ampu… "Exome… TRUE PUBLIC 0 2022-0… 160 TRUE ampca
4 blca_dfar… Blad… "Whole… TRUE PUBLIC 0 2022-0… 50 TRUE blca
5 blca_mskc… Blad… "Compr… TRUE PUBLIC 0 2022-0… 97 TRUE blca
6 blca_bgi Blad… "Whole… TRUE PUBLIC 0 2022-0… 99 TRUE blca
# … with 3 more variables: referenceGenome <chr>, pmid <chr>, citation <chr>,
# and abbreviated variable names ¹description, ²publicStudy, ³importDate,
# ⁴allSampleCount, ⁵readPermission, ⁶cancerTypeId</code></pre>
</div>
</div>
<p>We will use the following two studies for examples</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>all_studies <span class="sc">%>%</span></span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(studyId <span class="sc">%in%</span> <span class="fu">c</span>(<span class="st">"blca_nmibc_2017"</span>, <span class="st">"prad_msk_2019"</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 2 × 13
studyId name descr…¹ publi…² groups status impor…³ allSa…⁴ readP…⁵ cance…⁶
<chr> <chr> <chr> <lgl> <chr> <int> <chr> <int> <lgl> <chr>
1 blca_nmib… Nonm… IMPACT… TRUE PUBLIC 0 2022-0… 105 TRUE blca
2 prad_msk_… Pros… MSK-IM… TRUE PUBLIC 0 2022-0… 18 TRUE prosta…
# … with 3 more variables: referenceGenome <chr>, pmid <chr>, citation <chr>,
# and abbreviated variable names ¹description, ²publicStudy, ³importDate,
# ⁴allSampleCount, ⁵readPermission, ⁶cancerTypeId</code></pre>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb15"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="fu">get_study_info</span>(<span class="st">"blca_nmibc_2017"</span>) <span class="sc">%>%</span></span>
<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">t</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> [,1]
name "Nonmuscle Invasive Bladder Cancer (MSK Eur Urol 2017)"
description "IMPACT sequencing of 105 High Risk Nonmuscle Invasive Bladder Cancer samples."
publicStudy "TRUE"
pmid "28583311"
citation "Pietzak et al. Eur Urol 2017"
groups "PUBLIC"
status "0"
importDate "2022-08-17 22:59:50"
allSampleCount "105"
sequencedSampleCount "105"
cnaSampleCount "105"
mrnaRnaSeqSampleCount "0"
mrnaRnaSeqV2SampleCount "0"
mrnaMicroarraySampleCount "0"
miRnaSampleCount "0"
methylationHm27SampleCount "0"
rppaSampleCount "0"
massSpectrometrySampleCount "0"
completeSampleCount "0"
readPermission "TRUE"
studyId "blca_nmibc_2017"
cancerTypeId "blca"
cancerType.name "Bladder Urothelial Carcinoma"
cancerType.dedicatedColor "Yellow"
cancerType.shortName "BLCA"
cancerType.parent "bladder"
cancerType.cancerTypeId "blca"
referenceGenome "hg19" </code></pre>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb17"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>s1 <span class="ot"><-</span> <span class="fu">available_samples</span>(<span class="st">"blca_nmibc_2017"</span>) <span class="sc">%>%</span></span>
<span id="cb17-2"><a href="#cb17-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(sampleId, patientId, studyId) <span class="sc">%>%</span></span>
<span id="cb17-3"><a href="#cb17-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">head</span>(<span class="dv">10</span>)</span>
<span id="cb17-4"><a href="#cb17-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb17-5"><a href="#cb17-5" aria-hidden="true" tabindex="-1"></a>s2 <span class="ot"><-</span> <span class="fu">available_samples</span>(<span class="st">"prad_msk_2019"</span>) <span class="sc">%>%</span></span>
<span id="cb17-6"><a href="#cb17-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(sampleId, patientId, studyId) <span class="sc">%>%</span></span>
<span id="cb17-7"><a href="#cb17-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">head</span>(<span class="dv">10</span>)</span>
<span id="cb17-8"><a href="#cb17-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb17-9"><a href="#cb17-9" aria-hidden="true" tabindex="-1"></a>df_pairs <span class="ot"><-</span> <span class="fu">bind_rows</span>(s1, s2) <span class="sc">%>%</span></span>
<span id="cb17-10"><a href="#cb17-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(<span class="sc">-</span>patientId)</span>
<span id="cb17-11"><a href="#cb17-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb17-12"><a href="#cb17-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb17-13"><a href="#cb17-13" aria-hidden="true" tabindex="-1"></a>df_pairs <span class="ot"><-</span> df_pairs <span class="sc">%>%</span></span>
<span id="cb17-14"><a href="#cb17-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">rename</span>(<span class="st">"sample_id"</span> <span class="ot">=</span> sampleId,</span>
<span id="cb17-15"><a href="#cb17-15" aria-hidden="true" tabindex="-1"></a> <span class="st">"study_id"</span> <span class="ot">=</span> studyId)</span>
<span id="cb17-16"><a href="#cb17-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb17-17"><a href="#cb17-17" aria-hidden="true" tabindex="-1"></a>all_genomic <span class="ot"><-</span> <span class="fu">get_genetics_by_sample</span>(<span class="at">sample_study_pairs =</span> df_pairs)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Joining, by = "study_id"
The following parameters were used in query:
Study ID: "blca_nmibc_2017" and "prad_msk_2019"
Molecular Profile ID: blca_nmibc_2017_mutations and prad_msk_2019_mutations
Genes: "All available genes"
Joining, by = "study_id"
The following parameters were used in query:
Study ID: "blca_nmibc_2017" and "prad_msk_2019"
Molecular Profile ID: blca_nmibc_2017_cna and prad_msk_2019_cna
Genes: "All available genes"
Joining, by = "study_id"
The following parameters were used in query:
Study ID: "blca_nmibc_2017" and "prad_msk_2019"
Molecular Profile ID: blca_nmibc_2017_structural_variants and
prad_msk_2019_structural_variants
Genes: "All available genes"</code></pre>
</div>
</div>
</section>
<section id="processing-data" class="level1">
<h1>Processing Data</h1>
<p>Some research samples included in this study. We may want to check or ask if these were sampled on different (non IMPACT panels) and also we should get distributions of alterations.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb19"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a>s1_all <span class="ot"><-</span> <span class="fu">available_samples</span>(<span class="st">"blca_nmibc_2017"</span>) </span>
<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a>s1_all <span class="ot"><-</span> s1_all<span class="sc">$</span>sampleId</span>
<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb19-4"><a href="#cb19-4" aria-hidden="true" tabindex="-1"></a>s1_all[<span class="dv">90</span><span class="sc">:</span><span class="dv">105</span>]</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> [1] "P-0008234-T01-IM5" "P-0008240-T01-IM5" "P-0008734-T01-IM5"
[4] "P-0008834-T01-IM5" "P-0008867-T01-IM5" "P-0008880-T01-IM5"
[7] "P-0009371-T01-IM5" "P-0010271-T01-IM5" "P-0010316-T01-IM5"
[10] "P-0010531-T01-IM5" "s_DS_nmibc_007_P" "s_DS_nmibc_008_P"
[13] "s_DS_nmibc_010_P" "s_DS_nmibc_011_P" "s_DS_nmibc_014_P"
[16] "s_DS_nmibc_019_P" </code></pre>
</div>
</div>
<p>What type of genomic data is available?</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb21"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="fu">available_profiles</span>(<span class="st">"blca_nmibc_2017"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># A tibble: 3 × 8
molecularAlterationType datatype name descr…¹ showP…² patie…³ molec…⁴ studyId
<chr> <chr> <chr> <chr> <lgl> <lgl> <chr> <chr>
1 COPY_NUMBER_ALTERATION DISCRETE Puta… Copy N… TRUE FALSE blca_n… blca_n…
2 MUTATION_EXTENDED MAF Muta… Mutati… TRUE FALSE blca_n… blca_n…
3 STRUCTURAL_VARIANT SV Stru… Struct… TRUE FALSE blca_n… blca_n…
# … with abbreviated variable names ¹description, ²showProfileInAnalysisTab,
# ³patientLevel, ⁴molecularProfileId</code></pre>
</div>
</div>
<p>Get all genomic data:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb23"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a>all_genomic <span class="ot"><-</span> <span class="fu">get_genetics_by_study</span>(<span class="st">"blca_nmibc_2017"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>ℹ Returning all data for the "blca_nmibc_2017_mutations" molecular profile in the "blca_nmibc_2017" study</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>ℹ Returning all data for the "blca_nmibc_2017_cna" molecular profile in the "blca_nmibc_2017" study</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>ℹ Returning all data for the "blca_nmibc_2017_structural_variants" molecular profile in the "blca_nmibc_2017" study</code></pre>
</div>
</div>
<p>Note, you can also pull by Sample ID/Study ID pairs.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb27"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a>s1 <span class="ot"><-</span> <span class="fu">available_samples</span>(<span class="st">"blca_nmibc_2017"</span>) <span class="sc">%>%</span></span>
<span id="cb27-2"><a href="#cb27-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(sampleId, patientId, studyId) <span class="sc">%>%</span></span>
<span id="cb27-3"><a href="#cb27-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">head</span>(<span class="dv">10</span>)</span>
<span id="cb27-4"><a href="#cb27-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb27-5"><a href="#cb27-5" aria-hidden="true" tabindex="-1"></a>s2 <span class="ot"><-</span> <span class="fu">available_samples</span>(<span class="st">"prad_msk_2019"</span>) <span class="sc">%>%</span></span>
<span id="cb27-6"><a href="#cb27-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(sampleId, patientId, studyId) <span class="sc">%>%</span></span>
<span id="cb27-7"><a href="#cb27-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">head</span>(<span class="dv">10</span>)</span>
<span id="cb27-8"><a href="#cb27-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb27-9"><a href="#cb27-9" aria-hidden="true" tabindex="-1"></a>df_pairs <span class="ot"><-</span> <span class="fu">bind_rows</span>(s1, s2) <span class="sc">%>%</span></span>
<span id="cb27-10"><a href="#cb27-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(<span class="sc">-</span>patientId)</span>
<span id="cb27-11"><a href="#cb27-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb27-12"><a href="#cb27-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb27-13"><a href="#cb27-13" aria-hidden="true" tabindex="-1"></a>df_pairs <span class="ot"><-</span> df_pairs <span class="sc">%>%</span></span>
<span id="cb27-14"><a href="#cb27-14" aria-hidden="true" tabindex="-1"></a> <span class="fu">rename</span>(<span class="st">"sample_id"</span> <span class="ot">=</span> sampleId,</span>
<span id="cb27-15"><a href="#cb27-15" aria-hidden="true" tabindex="-1"></a> <span class="st">"study_id"</span> <span class="ot">=</span> studyId)</span>
<span id="cb27-16"><a href="#cb27-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb27-17"><a href="#cb27-17" aria-hidden="true" tabindex="-1"></a>all_genomic_by_sample <span class="ot"><-</span> <span class="fu">get_genetics_by_sample</span>(<span class="at">sample_study_pairs =</span> df_pairs, </span>
<span id="cb27-18"><a href="#cb27-18" aria-hidden="true" tabindex="-1"></a> <span class="at">genes =</span> <span class="st">"TP53"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Joining, by = "study_id"
The following parameters were used in query:
Study ID: "blca_nmibc_2017" and "prad_msk_2019"
Molecular Profile ID: blca_nmibc_2017_mutations and prad_msk_2019_mutations
Genes: "TP53"
Joining, by = "study_id"
The following parameters were used in query:
Study ID: "blca_nmibc_2017" and "prad_msk_2019"
Molecular Profile ID: blca_nmibc_2017_cna and prad_msk_2019_cna
Genes: "TP53"
Joining, by = "study_id"
The following parameters were used in query:
Study ID: "blca_nmibc_2017" and "prad_msk_2019"
Molecular Profile ID: blca_nmibc_2017_structural_variants and
prad_msk_2019_structural_variants
Genes: "TP53"</code></pre>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb29"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb29-1"><a href="#cb29-1" aria-hidden="true" tabindex="-1"></a>mutations <span class="ot"><-</span> all_genomic<span class="sc">$</span>mutation</span>
<span id="cb29-2"><a href="#cb29-2" aria-hidden="true" tabindex="-1"></a>cna <span class="ot"><-</span> all_genomic<span class="sc">$</span>cna</span>
<span id="cb29-3"><a href="#cb29-3" aria-hidden="true" tabindex="-1"></a>fusions <span class="ot"><-</span> all_genomic<span class="sc">$</span>structural_variant</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<p>Explore maf format (one row per mutation)</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb30"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb30-1"><a href="#cb30-1" aria-hidden="true" tabindex="-1"></a>mutations <span class="sc">%>%</span> <span class="fu">str</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>tibble [1,595 × 33] (S3: tbl_df/tbl/data.frame)
$ hugoGeneSymbol : chr [1:1595] "ABL1" "ABL1" "ABL1" "ABL1" ...
$ entrezGeneId : int [1:1595] 25 25 25 25 25 25 25 142 142 207 ...
$ uniqueSampleKey : chr [1:1595] "UC0wMDA1NjkwLVQwMS1JTTU6YmxjYV9ubWliY18yMDE3" "UC0wMDAzNDMzLVQwMS1JTTU6YmxjYV9ubWliY18yMDE3" "UC0wMDAzNDMzLVQwMS1JTTU6YmxjYV9ubWliY18yMDE3" "UC0wMDAzMjYxLVQwMS1JTTU6YmxjYV9ubWliY18yMDE3" ...
$ uniquePatientKey : chr [1:1595] "UC0wMDA1NjkwOmJsY2Ffbm1pYmNfMjAxNw" "UC0wMDAzNDMzOmJsY2Ffbm1pYmNfMjAxNw" "UC0wMDAzNDMzOmJsY2Ffbm1pYmNfMjAxNw" "UC0wMDAzMjYxOmJsY2Ffbm1pYmNfMjAxNw" ...
$ molecularProfileId : chr [1:1595] "blca_nmibc_2017_mutations" "blca_nmibc_2017_mutations" "blca_nmibc_2017_mutations" "blca_nmibc_2017_mutations" ...
$ sampleId : chr [1:1595] "P-0005690-T01-IM5" "P-0003433-T01-IM5" "P-0003433-T01-IM5" "P-0003261-T01-IM5" ...
$ patientId : chr [1:1595] "P-0005690" "P-0003433" "P-0003433" "P-0003261" ...
$ studyId : chr [1:1595] "blca_nmibc_2017" "blca_nmibc_2017" "blca_nmibc_2017" "blca_nmibc_2017" ...
$ center : chr [1:1595] "MSKCC" "MSKCC" "MSKCC" "MSKCC" ...
$ mutationStatus : chr [1:1595] "SOMATIC" "SOMATIC" "SOMATIC" "SOMATIC" ...
$ validationStatus : chr [1:1595] "Unknown" "Unknown" "Unknown" "Unknown" ...
$ tumorAltCount : int [1:1595] 46 226 226 89 28 82 98 266 26 118 ...
$ tumorRefCount : int [1:1595] 529 487 447 677 159 615 742 428 348 74 ...
$ normalAltCount : int [1:1595] 0 0 0 1 0 0 0 0 0 0 ...
$ normalRefCount : int [1:1595] 413 379 356 464 198 385 892 346 284 359 ...
$ startPosition : int [1:1595] 133738181 133760387 133760412 133760819 133759700 133738211 133759501 226566970 226567800 105246551 ...
$ endPosition : int [1:1595] 133738181 133760400 133760418 133760819 133759700 133738211 133759502 226566970 226567800 105246551 ...
$ referenceAllele : chr [1:1595] "C" "GCAGCCTCTGCAGG" "GAAAGCC" "G" ...
$ proteinChange : chr [1:1595] "T194I" "A904Efs*31" "G912_P914delinsAF" "E1048K" ...
$ mutationType : chr [1:1595] "Missense_Mutation" "Frame_Shift_Del" "In_Frame_Del" "Missense_Mutation" ...
$ functionalImpactScore: chr [1:1595] "" "" "" "" ...
$ fisValue : num [1:1595] 1.4e-45 1.4e-45 1.4e-45 1.4e-45 1.4e-45 ...
$ linkXvar : chr [1:1595] "" "" "" "" ...
$ linkPdb : chr [1:1595] "" "" "" "" ...
$ linkMsa : chr [1:1595] "" "" "" "" ...
$ ncbiBuild : chr [1:1595] "GRCh37" "GRCh37" "GRCh37" "GRCh37" ...
$ variantType : chr [1:1595] "SNP" "DEL" "DEL" "SNP" ...
$ keyword : chr [1:1595] "ABL1 T194 missense" "ABL1 truncating" NA "ABL1 E1048 missense" ...
$ chr : chr [1:1595] "9" "9" "9" "9" ...
$ variantAllele : chr [1:1595] "T" "-" "CTTT" "A" ...
$ refseqMrnaId : chr [1:1595] "NM_005157.4" "NM_005157.4" "NM_005157.4" "NM_005157.4" ...
$ proteinPosStart : int [1:1595] 194 904 912 1048 675 204 608 540 456 17 ...
$ proteinPosEnd : int [1:1595] 194 904 914 1048 675 204 610 540 456 17 ...</code></pre>
</div>
</div>
<section id="check-mutation-status" class="level2">
<h2 class="anchored" data-anchor-id="check-mutation-status">Check Mutation Status</h2>
<p>Sometimes you may want to code ‘Unknown’ as ‘Somatic’ (recall that somatic mutations can occur in any of the cells of the body except the germ cells and therefore are not passed on. These are often tumor-specific acquired mutations).</p>
<p>Researchers can compare tumor mutations to a matched normal sample. Tumor-normal comparisons are crucial for identifying the somatic variants that act as driver mutations in cancer progression</p>
<p>Filter out germline (unless working on germline study)</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb32"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb32-1"><a href="#cb32-1" aria-hidden="true" tabindex="-1"></a><span class="fu">table</span>(mutations<span class="sc">$</span>mutationStatus, <span class="at">useNA =</span> <span class="st">"always"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>
SOMATIC SOMATIC_VS_POOL UNKNOWN <NA>
1557 28 10 0 </code></pre>
</div>
</div>
</section>
<section id="zero-alteration-patients" class="level2">
<h2 class="anchored" data-anchor-id="zero-alteration-patients">Zero Alteration Patients</h2>
<p>Check if patients have zero alterations and be sure to include these patients in your final data set.</p>
<p>Example, these patients below have zero mutations.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb34"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb34-1"><a href="#cb34-1" aria-hidden="true" tabindex="-1"></a><span class="fu">setdiff</span>(s1_all, mutations<span class="sc">$</span>sampleId)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] "P-0003677-T01-IM5" "P-0005590-T01-IM5"</code></pre>
</div>
<div class="sourceCode cell-code" id="cb36"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb36-1"><a href="#cb36-1" aria-hidden="true" tabindex="-1"></a><span class="co"># if you queried, no mutations would come up</span></span>
<span id="cb36-2"><a href="#cb36-2" aria-hidden="true" tabindex="-1"></a><span class="fu">get_mutations_by_sample</span>(<span class="at">sample_id =</span> <span class="st">"P-0003677-T01-IM5"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>The following parameters were used in query:</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Study ID: "msk_impact_2017"</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Molecular Profile ID: "msk_impact_2017_mutations"</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>Genes: "All available genes"</code></pre>
</div>
<div class="cell-output cell-output-stdout">
<pre><code>NULL</code></pre>
</div>
</div>
</section>
<section id="create-gene-binary-matrix" class="level2">
<h2 class="anchored" data-anchor-id="create-gene-binary-matrix">Create Gene Binary Matrix</h2>
<p>Most genomic analyses start with a binary matrix of alterations. You can use <code>create_gene_binary()</code> following function in {gnomeR} (but be sure to check results!)</p>
<p>To use {gnomeR} functions, you need to do some data manipulation first.</p>
<p>!! NOTE: This may change in the upcoming months to be more user friendly.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb42"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb42-1"><a href="#cb42-1" aria-hidden="true" tabindex="-1"></a>mutations_clean <span class="ot"><-</span> <span class="fu">rename_columns</span>(mutations)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: `x` must be a one- or two-column data frame in `deframe()`.</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>! hugoGeneSymbol renamed Hugo_Symbol
! entrezGeneId renamed Entrez_Gene_Id
! center renamed Center
! ncbiBuild renamed NCBI_Build
! chr renamed Chromosome
! startPosition renamed Start_Position
! endPosition renamed End_Position
! mutationType renamed Variant_Classification
! variantType renamed Variant_Type
! referenceAllele renamed Reference_Allele
! sampleId renamed Tumor_Sample_Barcode
! validationStatus renamed Validation_Status
! mutationStatus renamed Mutation_Status
! proteinChange renamed HGVSp_Short
! variantAllele renamed Allele</code></pre>
</div>
<div class="sourceCode cell-code" id="cb45"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb45-1"><a href="#cb45-1" aria-hidden="true" tabindex="-1"></a>cna_clean <span class="ot"><-</span>cna <span class="sc">%>%</span></span>
<span id="cb45-2"><a href="#cb45-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="st">"hugo_symbol"</span> <span class="ot">=</span> hugoGeneSymbol) <span class="sc">%>%</span></span>
<span id="cb45-3"><a href="#cb45-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">reformat_cna</span>()</span>
<span id="cb45-4"><a href="#cb45-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb45-5"><a href="#cb45-5" aria-hidden="true" tabindex="-1"></a>fusions_clean <span class="ot"><-</span> fusions <span class="sc">%>%</span></span>
<span id="cb45-6"><a href="#cb45-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">rename</span>(<span class="st">"Hugo_Symbol"</span> <span class="ot">=</span> site1HugoSymbol) <span class="sc">%>%</span></span>
<span id="cb45-7"><a href="#cb45-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">rename_columns</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>Warning: `x` must be a one- or two-column data frame in `deframe()`.</code></pre>
</div>
<div class="cell-output cell-output-stderr">
<pre><code>! ncbiBuild renamed NCBI_Build
! sampleId renamed Tumor_Sample_Barcode</code></pre>
</div>
</div>
</section>
<section id="confirm-zero-patients-are-included-in-binary-matrix" class="level2">
<h2 class="anchored" data-anchor-id="confirm-zero-patients-are-included-in-binary-matrix">Confirm Zero Patients Are Included in Binary Matrix</h2>
<div class="cell">
<div class="sourceCode cell-code" id="cb48"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb48-1"><a href="#cb48-1" aria-hidden="true" tabindex="-1"></a>binmat1 <span class="ot"><-</span> <span class="fu">create_gene_binary</span>(</span>
<span id="cb48-2"><a href="#cb48-2" aria-hidden="true" tabindex="-1"></a> <span class="at">samples =</span> s1_all, </span>
<span id="cb48-3"><a href="#cb48-3" aria-hidden="true" tabindex="-1"></a> <span class="at">mutation =</span> mutations_clean</span>
<span id="cb48-4"><a href="#cb48-4" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb48-5"><a href="#cb48-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb48-6"><a href="#cb48-6" aria-hidden="true" tabindex="-1"></a><span class="fu">unique</span>(mutations_clean<span class="sc">$</span>Tumor_Sample_Barcode) <span class="sc">%>%</span> <span class="fu">length</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 103</code></pre>
</div>
</div>
<p>Samples arg should be specified!</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb50"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb50-1"><a href="#cb50-1" aria-hidden="true" tabindex="-1"></a>binmat2 <span class="ot"><-</span> <span class="fu">create_gene_binary</span>(</span>
<span id="cb50-2"><a href="#cb50-2" aria-hidden="true" tabindex="-1"></a><span class="co"># samples = s1_all, </span></span>
<span id="cb50-3"><a href="#cb50-3" aria-hidden="true" tabindex="-1"></a> <span class="at">mutation =</span> mutations_clean</span>
<span id="cb50-4"><a href="#cb50-4" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>ℹ `samples` argument is `NULL`. We will infer your cohort inclusion and resulting data frame will include all samples with at least one alteration in mutation, fusion or cna data frames</code></pre>
</div>
<div class="sourceCode cell-code" id="cb52"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb52-1"><a href="#cb52-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dim</span>(binmat1)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 105 320</code></pre>
</div>
<div class="sourceCode cell-code" id="cb54"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb54-1"><a href="#cb54-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dim</span>(binmat2)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 103 320</code></pre>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb56"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb56-1"><a href="#cb56-1" aria-hidden="true" tabindex="-1"></a><span class="fu">setdiff</span>(<span class="fu">rownames</span>(binmat1), <span class="fu">rownames</span>(binmat2))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] "P-0003677-T01-IM5" "P-0005590-T01-IM5"</code></pre>
</div>
</div>
<p>If you didn’t specify samples, your denominator may be under counted!</p>
</section>
<section id="annotate-nas-in-impact-panels" class="level2">
<h2 class="anchored" data-anchor-id="annotate-nas-in-impact-panels">Annotate NAs in IMPACT Panels</h2>
<p>Recall that there are several versions of the IMPACT panels. Not all genes are tested in all panels. We must account for this by inserting NAs for samples/genes that were not tested.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb58"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb58-1"><a href="#cb58-1" aria-hidden="true" tabindex="-1"></a><span class="fu">str_detect</span>(s1_all, <span class="st">"IM5"</span>) <span class="sc">%>%</span> <span class="fu">sum</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 97</code></pre>
</div>
<div class="sourceCode cell-code" id="cb60"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb60-1"><a href="#cb60-1" aria-hidden="true" tabindex="-1"></a><span class="fu">str_detect</span>(s1_all, <span class="st">"IM3"</span>) <span class="sc">%>%</span> <span class="fu">sum</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>[1] 2</code></pre>
</div>
</div>
<p>Let’s check what results look like before we specify panels:</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb62"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb62-1"><a href="#cb62-1" aria-hidden="true" tabindex="-1"></a>binmat <span class="ot"><-</span> <span class="fu">create_gene_binary</span>(</span>
<span id="cb62-2"><a href="#cb62-2" aria-hidden="true" tabindex="-1"></a> <span class="at">samples =</span> s1_all, </span>
<span id="cb62-3"><a href="#cb62-3" aria-hidden="true" tabindex="-1"></a> <span class="at">mutation =</span> mutations_clean, </span>
<span id="cb62-4"><a href="#cb62-4" aria-hidden="true" tabindex="-1"></a> <span class="at">cna =</span> cna_clean, </span>
<span id="cb62-5"><a href="#cb62-5" aria-hidden="true" tabindex="-1"></a> <span class="at">fusion =</span> fusions_clean</span>
<span id="cb62-6"><a href="#cb62-6" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb62-7"><a href="#cb62-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb62-8"><a href="#cb62-8" aria-hidden="true" tabindex="-1"></a><span class="fu">head</span>(binmat[<span class="dv">1</span><span class="sc">:</span><span class="dv">6</span>, <span class="dv">1</span><span class="sc">:</span><span class="dv">6</span>])</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> ABL1 PARP1 AKT1 ALK APC BIRC3
P-0001453-T01-IM3 1 0 0 0 1 0
P-0002166-T01-IM3 0 0 0 0 0 0
P-0003238-T01-IM5 0 0 0 0 0 0
P-0003257-T01-IM5 0 0 0 0 1 0
P-0003261-T01-IM5 1 0 0 0 1 0
P-0003352-T01-IM5 0 0 0 0 0 0</code></pre>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb64"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb64-1"><a href="#cb64-1" aria-hidden="true" tabindex="-1"></a>binmat <span class="ot"><-</span> binmat <span class="sc">%>%</span></span>
<span id="cb64-2"><a href="#cb64-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">rownames_to_column</span>(<span class="st">"sample_id"</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="cb65"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb65-1"><a href="#cb65-1" aria-hidden="true" tabindex="-1"></a><span class="fu">map_dbl</span>(binmat, <span class="sc">~</span><span class="fu">sum</span>(<span class="fu">is.na</span>(.x)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> sample_id ABL1 PARP1 AKT1 ALK APC BIRC3
0 0 0 0 0 0 0
AR RHOA ZFHX3 ATM ATR ATRX AXL
0 0 0 0 0 0 0
BARD1 CCND1 BCL6 PRDM1 BLM BMPR1A FOXL2
0 0 0 0 0 0 0
BRCA1 BRAF BRCA2 CALR CASP8 RUNX1 CCND2
0 0 0 0 0 0 0
CCND3 CDH1 CDK8 CDKN1A CDKN1B CDKN2A CEBPA
0 0 0 0 0 0 0
CHEK1 CREBBP CRKL CSF3R CTNNB1 DAXX DNMT1
0 0 0 0 0 0 0
DNMT3A DNMT3B E2F3 EGFR EIF4E EP300 EPHA3
0 0 0 0 0 0 0
EPHA5 EPHA7 EPHB1 ERBB2 ERBB3 ERBB4 ERCC2
0 0 0 0 0 0 0
ERCC4 ERCC5 ERG ESR1 ETV1 ETV6 EZH2
0 0 0 0 0 0 0
FANCA FANCC FAT1 FGF4 FGFR1 FGFR3 FGFR2
0 0 0 0 0 0 0
FGFR4 FH FOXO1 FLT1 FLT3 FLT4 MTOR
0 0 0 0 0 0 0
FYN GATA2 GATA3 GLI1 GNAQ GNAS GPS2
0 0 0 0 0 0 0
GRIN2A GSK3B MSH6 H1-2 H3-3A H3-3B HGF
0 0 0 0 0 0 0
FOXA1 HRAS DNAJB1 IDH1 IGF1R IGF2 IL7R
0 0 0 0 0 0 0
IL10 INHBA INPP4A INSR INSRR IRF4 IRS1
0 0 0 0 0 0 0
JAK1 JAK2 JAK3 JUN KDR KIT KRAS
0 0 0 0 0 0 0
LMO1 SH2D1A SMAD2 SMAD4 MAX MCL1 MDM2
0 0 0 0 0 0 0
MDM4 MAP3K1 MEN1 MET MITF MLH1 KMT2A
0 0 0 0 0 0 0
MPL MSH2 MST1 MST1R MUTYH MYC MYCL
0 0 0 0 0 0 0
MYCN MYD88 MYOD1 NBN NF1 NF2 NFE2L2
0 0 0 0 0 0 0
NFKBIA NOTCH1 NOTCH2 NOTCH3 NOTCH4 NPM1 NRAS
0 0 0 0 0 0 0
NTRK1 NTRK3 PAK1 PDGFRA PDGFRB PGR PIK3C2G
0 0 0 0 0 0 0
PIK3C3 PIK3CA PIK3CB PIK3CG PIK3R1 PIK3R2 PLCG2
0 0 0 0 0 0 0
PMS1 PMS2 POLD1 POLE PPP2R1A PPP6C PRKAR1A
0 0 0 0 0 0 0
MAPK1 PTCH1 PTEN PTPRD PTPRS RAC1 RAD21
0 0 0 0 0 0 0
RAD51 RAD51C RAD51B RAD51D RAD52 RAF1 RARA
0 0 0 0 0 0 0
RASA1 RB1 KDM5A REL RET RHEB RIT1
0 0 0 0 0 0 0
ROS1 RPS6KB2 SDHA SDHD SRSF2 SMARCA4 SMARCB1
0 0 0 0 0 0 0
SMARCD1 SMO SOX2 SOX9 SRC STAT3 STAT5A
0 0 0 0 0 0 0
AURKA STK11 SYK TBX3 TCF7L2 TERT TGFBR1
0 0 0 0 0 0 0
TGFBR2 TMPRSS2 TP53 TRAF2 TSC1 TSC2 TSHR
0 0 0 0 0 0 0
U2AF1 KDM6A VEGFA VHL WT1 XPO1 YES1
0 0 0 0 0 0 0
CXCR4 KMT2D NCOA3 RBM10 KDM5C ARID1A AXIN2
0 0 0 0 0 0 0
BAP1 H3C4 H3C3 H3C8 H3C10 H3C2 SPOP
0 0 0 0 0 0 0
RAD54L CUL3 TP63 IRS2 EED INPP4B FUBP1
0 0 0 0 0 0 0
BCL10 PHOX2B H3C7 RPS6KA4 LATS1 MAP3K13 KLF4
0 0 0 0 0 0 0
RECQL4 NCOR1 IKBKE MDC1 NUP93 KEAP1 FGF19
0 0 0 0 0 0 0
MED12 AKT3 BCL2L11 SH2B3 RAD50 IKZF1 CTCF
0 0 0 0 0 0 0
STAG2 PLK2 MALT1 PNRC1 PTPRT CHEK2 DIS3
0 0 0 0 0 0 0
SPEN CIC MGA ICOSLG DICER1 SF3B1 BRD4
0 0 0 0 0 0 0
SUZ12 TIMM8B LATS2 GREM1 FOXP1 BBC3 SETD2
0 0 0 0 0 0 0
ANKRD11 SUFU CDK12 ERRFI1 TET2 BCOR RNF43
0 0 0 0 0 0 0
SHQ1 PBRM1 ASXL2 FBXW7 PAK5 ARID1B RPTOR
0 0 0 0 0 0 0
KMT2C CRLF2 NSD1 COP1 PALB2 TET1 FIP1L1
0 0 0 0 0 0 0
STK40 BRIP1 ABRAXAS1 ARID5B TRAF7 CARD11 DOT1L
0 0 0 0 0 0 0
AMER1 ASXL1 ARID2 RICTOR H3C13 MEF2B TACC3.fus
0 0 0 0 0 0 0
EP300.fus NA.fus RAB35.fus RUNX1.fus FANCA.fus FGFR3.fus BRAF.fus
0 0 0 0 0 0 0
MAP2K1.fus CDKN2A.fus MDM2.Amp RB1.Del ATRX.Amp PTPRD.Del CDKN2A.Del
0 0 0 0 0 0 0
ATM.Del CDKN2B.Del FGF19.Amp CCND1.Amp FGF4.Amp FGF3.Amp INPP4A.Amp
0 0 0 0 0 0 0
DDR2.Amp SDHC.Amp COP1.Amp EPHA3.Del EP300.Del ERBB2.Amp CDK12.Amp
0 0 0 0 0 0 0
FGFR1.Amp FGFR1.Del SRC.Amp FGFR3.Amp TBX3.Amp U2AF1.Del BARD1.Del
0 0 0 0 0 0 0
CXCR4.Del SH2B3.Amp PTPN11.Amp RAB35.Amp CDKN1B.Del DIS3.Del EPHA5.Del
0 0 0 0 0 0 0
PAK1.Amp PPM1D.Amp MCL1.Amp RAF1.Amp VHL.Amp PAX5.Del PPP6C.Del
0 0 0 0 0 0 0
EED.Amp NF2.Amp NOTCH2.Amp MYCL.Amp PRDM1.Amp E2F3.Amp NKX3-1.Del
0 0 0 0 0 0 0
SOCS1.Amp CDK4.Amp SH2D1A.Del STAG2.Del FOXP1.Del GRIN2A.Amp H3C13.Amp
0 0 0 0 0 0 0
H3C14.Amp RICTOR.Amp SDHA.Amp IL7R.Amp TERT.Amp PTCH1.Del RIT1.Amp
0 0 0 0 0 0 0
CEBPA.Amp CRLF2.Amp CD274.Del JAK2.Del GATA3.Amp FAT1.Del RAD21.Del
0 0 0 0 0 0 0
XPO1.Amp NKX2-1.Del NFKBIA.Del MAPK3.Amp PGR.Del CHEK1.Del FOXA1.Amp
0 0 0 0 0 0 0
FOXA1.Del YAP1.Del KMT2A.Del SDHD.Del MRE11.Del BIRC3.Del CBL.Del
0 0 0 0 0 0 0
CCND3.Amp CHEK2.Amp IDH1.Amp
0 0 0 </code></pre>
</div>
</div>
<p>Use the <code>specify_panel</code> argument to take care of NA annotation for you!</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb67"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb67-1"><a href="#cb67-1" aria-hidden="true" tabindex="-1"></a>binmat_panel <span class="ot"><-</span> <span class="fu">create_gene_binary</span>(</span>
<span id="cb67-2"><a href="#cb67-2" aria-hidden="true" tabindex="-1"></a> <span class="at">samples =</span> s1_all, </span>
<span id="cb67-3"><a href="#cb67-3" aria-hidden="true" tabindex="-1"></a> <span class="at">mutation =</span> mutations_clean, </span>
<span id="cb67-4"><a href="#cb67-4" aria-hidden="true" tabindex="-1"></a> <span class="at">cna =</span> cna_clean, </span>
<span id="cb67-5"><a href="#cb67-5" aria-hidden="true" tabindex="-1"></a> <span class="at">fusion =</span> fusions_clean, </span>
<span id="cb67-6"><a href="#cb67-6" aria-hidden="true" tabindex="-1"></a> <span class="at">specify_panel =</span> <span class="st">"impact"</span></span>
<span id="cb67-7"><a href="#cb67-7" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>→ Couldn't infer IMPACT panel version from these sample_ids, therefore no NA panel annotation will be done for these: s_DS_nmibc_007_P, s_DS_nmibc_008_P, s_DS_nmibc_010_P, s_DS_nmibc_011_P, s_DS_nmibc_014_P, and s_DS_nmibc_019_P</code></pre>
</div>
<div class="sourceCode cell-code" id="cb69"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb69-1"><a href="#cb69-1" aria-hidden="true" tabindex="-1"></a><span class="fu">map_dbl</span>(binmat_panel, <span class="sc">~</span><span class="fu">sum</span>(<span class="fu">is.na</span>(.x))) <span class="sc">%>%</span> <span class="fu">head</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> ABL1 PARP1 AKT1 ALK APC BIRC3
6 6 6 6 6 8 </code></pre>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb71"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb71-1"><a href="#cb71-1" aria-hidden="true" tabindex="-1"></a>sample_panel_pair <span class="ot"><-</span> binmat <span class="sc">%>%</span></span>
<span id="cb71-2"><a href="#cb71-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(sample_id)</span>
<span id="cb71-3"><a href="#cb71-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb71-4"><a href="#cb71-4" aria-hidden="true" tabindex="-1"></a>sample_panel_pair <span class="ot"><-</span> sample_panel_pair <span class="sc">%>%</span></span>
<span id="cb71-5"><a href="#cb71-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">panel_id =</span> <span class="fu">case_when</span>(</span>
<span id="cb71-6"><a href="#cb71-6" aria-hidden="true" tabindex="-1"></a> stringr<span class="sc">::</span><span class="fu">str_detect</span>(.data<span class="sc">$</span>sample_id, <span class="st">"-IM3"</span>) <span class="sc">~</span> <span class="st">"IMPACT341"</span>,</span>
<span id="cb71-7"><a href="#cb71-7" aria-hidden="true" tabindex="-1"></a> stringr<span class="sc">::</span><span class="fu">str_detect</span>(.data<span class="sc">$</span>sample_id, <span class="st">"-IM5"</span>) <span class="sc">~</span> <span class="st">"IMPACT410"</span>,</span>
<span id="cb71-8"><a href="#cb71-8" aria-hidden="true" tabindex="-1"></a> stringr<span class="sc">::</span><span class="fu">str_detect</span>(.data<span class="sc">$</span>sample_id, <span class="st">"-IM6"</span>) <span class="sc">~</span> <span class="st">"IMPACT468"</span>,</span>
<span id="cb71-9"><a href="#cb71-9" aria-hidden="true" tabindex="-1"></a> stringr<span class="sc">::</span><span class="fu">str_detect</span>(.data<span class="sc">$</span>sample_id, <span class="st">"-IM7"</span>) <span class="sc">~</span> <span class="st">"IMPACT505"</span>,</span>
<span id="cb71-10"><a href="#cb71-10" aria-hidden="true" tabindex="-1"></a> <span class="cn">TRUE</span> <span class="sc">~</span> <span class="st">"IMPACT505"</span></span>
<span id="cb71-11"><a href="#cb71-11" aria-hidden="true" tabindex="-1"></a> ))</span>
<span id="cb71-12"><a href="#cb71-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb71-13"><a href="#cb71-13" aria-hidden="true" tabindex="-1"></a>binmat_panel <span class="ot"><-</span> <span class="fu">create_gene_binary</span>(</span>
<span id="cb71-14"><a href="#cb71-14" aria-hidden="true" tabindex="-1"></a> <span class="at">samples =</span> s1_all, </span>
<span id="cb71-15"><a href="#cb71-15" aria-hidden="true" tabindex="-1"></a> <span class="at">mutation =</span> mutations_clean, </span>
<span id="cb71-16"><a href="#cb71-16" aria-hidden="true" tabindex="-1"></a> <span class="at">cna =</span> cna_clean, </span>
<span id="cb71-17"><a href="#cb71-17" aria-hidden="true" tabindex="-1"></a> <span class="at">fusion =</span> fusions_clean, </span>
<span id="cb71-18"><a href="#cb71-18" aria-hidden="true" tabindex="-1"></a> <span class="at">specify_panel =</span> sample_panel_pair</span>
<span id="cb71-19"><a href="#cb71-19" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb71-20"><a href="#cb71-20" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb71-21"><a href="#cb71-21" aria-hidden="true" tabindex="-1"></a><span class="fu">map_dbl</span>(binmat_panel, <span class="sc">~</span><span class="fu">sum</span>(<span class="fu">is.na</span>(.x))) <span class="sc">%>%</span> <span class="fu">head</span>(<span class="dv">50</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code> ABL1 PARP1 AKT1 ALK APC BIRC3 AR RHOA ZFHX3 ATM ATR
0 0 0 0 0 2 0 0 2 0 0
ATRX AXL BARD1 CCND1 BCL6 PRDM1 BLM BMPR1A FOXL2 BRCA1 BRAF
0 0 0 0 0 0 0 0 0 0 0
BRCA2 CALR CASP8 RUNX1 CCND2 CCND3 CDH1 CDK8 CDKN1A CDKN1B CDKN2A
0 2 0 0 0 0 0 0 0 0 0
CEBPA CHEK1 CREBBP CRKL CSF3R CTNNB1 DAXX DNMT1 DNMT3A DNMT3B E2F3
2 0 0 0 2 0 0 0 0 0 0
EGFR EIF4E EP300 EPHA3 EPHA5 EPHA7
0 2 0 0 0 2 </code></pre>
</div>
</div>
<section id="recode-aliases" class="level3">
<h3 class="anchored" data-anchor-id="recode-aliases">Recode Aliases</h3>
<p>recode alias argument helps check for any genes that have been renamed.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb73"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb73-1"><a href="#cb73-1" aria-hidden="true" tabindex="-1"></a>binmat_panel_recode <span class="ot"><-</span> <span class="fu">create_gene_binary</span>(</span>
<span id="cb73-2"><a href="#cb73-2" aria-hidden="true" tabindex="-1"></a> <span class="at">samples =</span> s1_all, </span>
<span id="cb73-3"><a href="#cb73-3" aria-hidden="true" tabindex="-1"></a> <span class="at">mutation =</span> mutations_clean, </span>
<span id="cb73-4"><a href="#cb73-4" aria-hidden="true" tabindex="-1"></a> <span class="at">cna =</span> cna_clean, </span>
<span id="cb73-5"><a href="#cb73-5" aria-hidden="true" tabindex="-1"></a> <span class="at">fusion =</span> fusions_clean, </span>
<span id="cb73-6"><a href="#cb73-6" aria-hidden="true" tabindex="-1"></a> <span class="at">specify_panel =</span> sample_panel_pair, </span>
<span id="cb73-7"><a href="#cb73-7" aria-hidden="true" tabindex="-1"></a> <span class="at">recode_aliases =</span> <span class="cn">TRUE</span></span>
<span id="cb73-8"><a href="#cb73-8" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
</section>
</section>
</section>
<section id="analyzing-data" class="level1">
<h1>Analyzing Data</h1>
<p>Now that we’ve processed the data we will summarize it. You can use <code>tbl_summary()</code> or the following experimental function which has some benefits:</p>
<ul>
<li>automatically orders genes by frequency</li>
<li>allows you to specify a prevalence threshold cutoff</li>
</ul>
<div class="cell">
<div class="sourceCode cell-code" id="cb74"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb74-1"><a href="#cb74-1" aria-hidden="true" tabindex="-1"></a><span class="fu">tbl_genomic</span>(binmat_panel, <span class="at">freq_cutoff =</span> .<span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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