Commit 1fef5a43 authored by Olivier Rue's avatar Olivier Rue
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curation D1D2 WINE

parent 6fa17659
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......@@ -11,7 +11,7 @@
<meta name="author" content="Olivier Rué" />
<meta name="date" content="2022-01-03" />
<meta name="date" content="2022-01-12" />
<title>Real samples analysis</title>
......@@ -279,7 +279,7 @@ div.tocify {
<h1 class="title toc-ignore">Real samples analysis</h1>
<h4 class="author">Olivier Rué</h4>
<h4 class="date">2022-01-03</h4>
<h4 class="date">2022-01-12</h4>
</div>
......@@ -475,7 +475,7 @@ saveRDS(physeq_rpb2_final,&quot;REAL_MEAT/RPB2_final.rds&quot;)</code></pre>
<pre class="r"><code>#if (!file.exists(&quot;REAL_MEAT/meat_final.rds&quot;)){
meat_all_final &lt;- merge_phyloseq(physeq_its1_final, physeq_its2_final, physeq_d1d2_final, physeq_rpb2_final)
sample_data(meat_all_final)$Marker &lt;- factor(sample_data(meat_all_final)$Marker, levels=c(&quot;ITS1&quot;,&quot;ITS2&quot;,&quot;D1D2&quot;,&quot;RPB2&quot;))
saveRDS(meat_all_final,&quot;REAL_WINE/meat_final.rds&quot;)
saveRDS(meat_all_final,&quot;REAL_MEAT/meat_final.rds&quot;)
#}else{
# meat_all_final &lt;- readRDS(&quot;REAL_MEAT/meat_final.rds&quot;)
#}</code></pre>
......@@ -1189,13 +1189,13 @@ ggVennDiagram(x,label_alpha = 0) +
#physeq_its2_final &lt;- curation_wine_its2(physeq_its2)
#saveRDS(physeq_its2_final,&quot;REAL_WINE/ITS2_final.rds&quot;)
#physeq_d1d2_final &lt;- curation_wine_d1d2(physeq_d1d2)
#saveRDS(physeq_d1d2_final,&quot;REAL_WINE/D1D2_final.rds&quot;)
physeq_d1d2_final &lt;- curation_wine_d1d2(physeq_d1d2)
saveRDS(physeq_d1d2_final,&quot;REAL_WINE/D1D2_final.rds&quot;)
physeq_rpb2_final &lt;- curation_wine_rpb2(physeq_rpb2)
saveRDS(physeq_rpb2_final,&quot;REAL_WINE/RPB2_final.rds&quot;)</code></pre>
<pre class="r"><code>#if (!file.exists(&quot;REAL_WINE/wine_final.rds&quot;)){
wine_all_final &lt;- merge_phyloseq(physeq_its1, physeq_its2, physeq_d1d2, physeq_rpb2_final)
wine_all_final &lt;- merge_phyloseq(physeq_its1, physeq_its2, physeq_d1d2_final, physeq_rpb2_final)
sample_data(wine_all_final)$Marker &lt;- factor(sample_data(wine_all_final)$Marker, levels=c(&quot;ITS1&quot;,&quot;ITS2&quot;,&quot;D1D2&quot;,&quot;RPB2&quot;))
saveRDS(wine_all_final,&quot;REAL_WINE/wine_final.rds&quot;)
#}else{
......
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