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Add back in Gliomatosis Cerebri; rerun
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jaclyn-taroni committed Sep 25, 2020
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3 changes: 2 additions & 1 deletion analyses/molecular-subtyping-HGG/00-HGG-select-pathology-dx.Rmd
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Expand Up @@ -107,7 +107,8 @@ For the CBTTC samples, the `pathology_diagnosis` fields are harmonized, so we ca
```{r}
exact_path_dx<- c(
"High-grade glioma/astrocytoma (WHO grade III/IV)",
"Brainstem glioma- Diffuse intrinsic pontine glioma"
"Brainstem glioma- Diffuse intrinsic pontine glioma",
"Gliomatosis Cerebri"
)
```

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52 changes: 25 additions & 27 deletions analyses/molecular-subtyping-HGG/00-HGG-select-pathology-dx.nb.html
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6 changes: 3 additions & 3 deletions analyses/molecular-subtyping-HGG/03-HGG-molecular-subtyping-cnv.nb.html
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Expand Up @@ -3061,7 +3061,7 @@ <h4>Inclusion Criteria</h4>
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<p>We’d then expect 119 samples to have non-NA values in the cleaned CNV files.</p>
<p>We’d then expect 121 samples to have non-NA values in the cleaned CNV files.</p>
</div>
<div id="read-in-cn-data" class="section level4">
<h4>Read in CN Data</h4>
Expand Down Expand Up @@ -3233,8 +3233,8 @@ <h2>Join Together</h2>
<!-- rnb-source-begin eyJkYXRhIjoibnJvdyhmaW5hbF9oZ2dfY25fZGYpIn0= -->
<pre class="r"><code>nrow(final_hgg_cn_df)</code></pre>
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<pre><code>[1] 119</code></pre>
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<pre><code>[1] 121</code></pre>
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8 changes: 4 additions & 4 deletions analyses/molecular-subtyping-HGG/04-HGG-molecular-subtyping-mutation.nb.html
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Expand Up @@ -3136,9 +3136,9 @@ <h4>Coding mutations in genes other than <em>TERT</em></h4>
dplyr::filter(Variant_Classification != &quot;Silent&quot;,
Hugo_Symbol != &quot;TERT&quot;)</code></pre>
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<pre><code>Ratio of variants in this BED: 4.449254
Ratio of variants being filtered out: -3.449254 </code></pre>
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<pre><code>Ratio of variants in this BED: 4.442623
Ratio of variants being filtered out: -3.442623 </code></pre>
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<!-- rnb-source-begin eyJkYXRhIjoiaGVhZChjb2Rpbmdfc252X2RmLCBuID0gMTApIn0= -->
<pre class="r"><code>head(coding_snv_df, n = 10)</code></pre>
Expand All @@ -3165,7 +3165,7 @@ <h4><em>TERT</em> mutation</h4>
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4 changes: 2 additions & 2 deletions analyses/molecular-subtyping-HGG/05-HGG-molecular-subtyping-fusion.nb.html
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Expand Up @@ -3057,7 +3057,7 @@ <h2>Filter and Wrangle Fusion Data</h2>
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