Fix error in pull command

Author: AshKernow

Markdowns/12_Gene_set_testing.Solutions.Rmd

@@ -38,7 +38,7 @@ shrink.d11 <- readRDS("RObjects/Shrunk_Results.d11.rds")
 logFC <- shrink.d11 %>% 
   drop_na(FDR, Entrez) %>% 
   filter(FDR < 0.01) %>% 
-  pull(Entrez, logFC) 
+  pull(logFC, Entrez) 
 
 pathview(gene.data = logFC, 
          pathway.id = "mmu04659", 

Markdowns/12_Gene_set_testing.Solutions.html

@@ -201,14 +201,14 @@ <h2>Exercise 1 - pathview</h2>
 <pre class="r"><code>logFC &lt;- shrink.d11 %&gt;% 
   drop_na(FDR, Entrez) %&gt;% 
   filter(FDR &lt; 0.01) %&gt;% 
-  pull(Entrez, logFC) 
+  pull(logFC, Entrez) 
 
 pathview(gene.data = logFC, 
          pathway.id = &quot;mmu04659&quot;, 
          species = &quot;mmu&quot;, 
          limit = list(gene=5, cpd=1))</code></pre>
-<pre><code>## Warning: None of the genes or compounds mapped to the pathway!
-## Argument gene.idtype or cpd.idtype may be wrong.</code></pre>
+<pre><code>## Info: Downloading xml files for mmu04659, 1/1 pathways..</code></pre>
+<pre><code>## Info: Downloading png files for mmu04659, 1/1 pathways..</code></pre>
 <pre><code>## &#39;select()&#39; returned 1:1 mapping between keys and columns</code></pre>
 <pre><code>## Info: Working in directory /Users/sawle01/Documents/training/Bulk_RNAseq_Course_Base/Markdowns</code></pre>
 <pre><code>## Info: Writing image file mmu04659.pathview.png</code></pre>
@@ -310,8 +310,8 @@ <h2>Exercise 3 - GSEA</h2>
   select(-core_enrichment) %&gt;%
   mutate(across(c(&quot;enrichmentScore&quot;, &quot;NES&quot;), round, digits=3)) %&gt;% 
   mutate(across(c(&quot;pvalue&quot;, &quot;p.adjust&quot;, &quot;qvalues&quot;), scales::scientific))</code></pre>
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 <blockquote>
 <ol start="3" style="list-style-type: decimal">
 <li>Conduct the same analysis for the day 33 Infected vs Uninfected contrast.</li>
@@ -336,7 +336,7 @@ <h2>Exercise 3 - GSEA</h2>
                 maxGSSize = 500)</code></pre>
 <pre><code>## preparing geneSet collections...</code></pre>
 <pre><code>## GSEA analysis...</code></pre>
-<pre><code>## Warning in fgseaMultilevel(...): There were 4 pathways for which P-values were
+<pre><code>## Warning in fgseaMultilevel(...): There were 2 pathways for which P-values were
 ## not calculated properly due to unbalanced (positive and negative) gene-level
 ## statistic values. For such pathways pval, padj, NES, log2err are set to NA. You
 ## can try to increase the value of the argument nPermSimple (for example set it
@@ -352,8 +352,8 @@ <h2>Exercise 3 - GSEA</h2>
   select(-core_enrichment) %&gt;%
   mutate(across(c(&quot;enrichmentScore&quot;, &quot;NES&quot;), round, digits=3)) %&gt;% 
   mutate(across(c(&quot;pvalue&quot;, &quot;p.adjust&quot;, &quot;qvalues&quot;), scales::scientific))</code></pre>
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 </div>