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            <h1 id="seo-header">TCGA (三) 两组间DEGs分析</h1>
            
            
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                <h2 id="第一步-读取数据"><a href="#第一步-读取数据" class="headerlink" title="第一步 读取数据"></a>第一步 读取数据</h2><ul>
<li>TCGA</li>
</ul>
<figure class="highlight haskell"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br><span class="line">66</span><br><span class="line">67</span><br><span class="line">68</span><br><span class="line">69</span><br><span class="line">70</span><br></pre></td><td class="code"><pre><code class="hljs haskell"><span class="hljs-title">library</span>(<span class="hljs-type">TCGAbiolinks</span>)<br><span class="hljs-title">library</span>(plyr)<br><span class="hljs-title">library</span>(limma)<br><span class="hljs-title">library</span>(biomaRt)<br><span class="hljs-title">library</span>(<span class="hljs-type">SummarizedExperiment</span>)<br><br><span class="hljs-meta"># 配置数据路径</span><br><span class="hljs-title">root_path</span> = <span class="hljs-string">&quot;~/zlliu/R_data/TCGA&quot;</span><br> <br><span class="hljs-meta"># 配置结果保存路径</span><br><span class="hljs-title">output_path</span> = root_path<br><span class="hljs-title">if</span> (!file.exists(output_path))&#123;dir.create(output_path)&#125;<br> <br><span class="hljs-meta"># 设置工作目录，输出文件将保存在此目录下</span><br><span class="hljs-title">setwd</span>(output_path)<br><span class="hljs-title">getwd</span>()<br><br><span class="hljs-meta"># 一般的前列腺癌 GDC Data Portal 是 hg38 的</span><br><span class="hljs-type">PRAD</span> &lt;- <span class="hljs-type">GDCquery</span>(project = &#x27;<span class="hljs-type">TCGA</span>-<span class="hljs-type">PRAD&#x27;</span>,<br>                  <span class="hljs-class"><span class="hljs-keyword">data</span>.category = &quot;<span class="hljs-type">Transcriptome</span> <span class="hljs-type">Profiling</span>&quot;,</span><br>                  <span class="hljs-class"><span class="hljs-keyword">data</span>.<span class="hljs-keyword">type</span> = &quot;<span class="hljs-type">Gene</span> <span class="hljs-type">Expression</span> <span class="hljs-type">Quantification</span>&quot;, </span><br>                  workflow.<span class="hljs-class"><span class="hljs-keyword">type</span> = &quot;<span class="hljs-type">HTSeq</span> - <span class="hljs-type">Counts</span>&quot;)</span><br><span class="hljs-meta"># mCRPC</span><br><span class="hljs-title">mCRPC</span> &lt;- <span class="hljs-type">GDCquery</span>(project = &#x27;<span class="hljs-type">WCDT</span>-<span class="hljs-type">MCRPC&#x27;</span>,<br>              <span class="hljs-class"><span class="hljs-keyword">data</span>.category = &quot;<span class="hljs-type">Transcriptome</span> <span class="hljs-type">Profiling</span>&quot;,</span><br>              <span class="hljs-class"><span class="hljs-keyword">data</span>.<span class="hljs-keyword">type</span> = &quot;<span class="hljs-type">Gene</span> <span class="hljs-type">Expression</span> <span class="hljs-type">Quantification</span>&quot;, </span><br>              workflow.<span class="hljs-class"><span class="hljs-keyword">type</span> = &quot;<span class="hljs-type">HTSeq</span> - <span class="hljs-type">Counts</span>&quot;)</span><br> <br><span class="hljs-meta"># 选择病例列 ，不加cols参数则是完整结果的全部列</span><br><span class="hljs-type">PRAD_cases</span> &lt;- getResults(<span class="hljs-type">PRAD</span>,cols=c(<span class="hljs-string">&quot;cases&quot;</span>))<br><span class="hljs-title">mCRPC_cases</span> &lt;- getResults(mCRPC,cols=c(<span class="hljs-string">&quot;cases&quot;</span>))<br> <br><span class="hljs-meta"># 选择癌组织数据</span><br><span class="hljs-type">PRAD_tp</span>  &lt;- <span class="hljs-type">TCGAquery_SampleTypes</span>(barcode = <span class="hljs-type">PRAD_cases</span>, typesample = <span class="hljs-string">&quot;TP&quot;</span>)<br> <br><span class="hljs-type">PRAD_D</span> &lt;- <span class="hljs-type">GDCquery</span>(project = &#x27;<span class="hljs-type">TCGA</span>-<span class="hljs-type">PRAD&#x27;</span>,<br>                  <span class="hljs-class"><span class="hljs-keyword">data</span>.category = &quot;<span class="hljs-type">Transcriptome</span> <span class="hljs-type">Profiling</span>&quot;,</span><br>                  <span class="hljs-class"><span class="hljs-keyword">data</span>.<span class="hljs-keyword">type</span> = &quot;<span class="hljs-type">Gene</span> <span class="hljs-type">Expression</span> <span class="hljs-type">Quantification</span>&quot;, </span><br>                  workflow.<span class="hljs-class"><span class="hljs-keyword">type</span> = &quot;<span class="hljs-type">HTSeq</span> - <span class="hljs-type">Counts</span>&quot;,</span><br>                  barcode = <span class="hljs-type">PRAD_tp</span>)<br><span class="hljs-title">mCRPC_D</span> &lt;- <span class="hljs-type">GDCquery</span>(project = &#x27;<span class="hljs-type">WCDT</span>-<span class="hljs-type">MCRPC&#x27;</span>,<br>              <span class="hljs-class"><span class="hljs-keyword">data</span>.category = &quot;<span class="hljs-type">Transcriptome</span> <span class="hljs-type">Profiling</span>&quot;,</span><br>              <span class="hljs-class"><span class="hljs-keyword">data</span>.<span class="hljs-keyword">type</span> = &quot;<span class="hljs-type">Gene</span> <span class="hljs-type">Expression</span> <span class="hljs-type">Quantification</span>&quot;, </span><br>              workflow.<span class="hljs-class"><span class="hljs-keyword">type</span> = &quot;<span class="hljs-type">HTSeq</span> - <span class="hljs-type">Counts</span>&quot;,</span><br>              sample.<span class="hljs-class"><span class="hljs-keyword">type</span> = &quot;<span class="hljs-type">Metastatic</span>&quot;, #下载癌组织的数据</span><br>              barcode = mCRPC_cases)<br><span class="hljs-title">saveRDS</span>(<span class="hljs-type">PRAD_D</span>,<span class="hljs-string">&quot;PRAD_D.rds&quot;</span>)<br><span class="hljs-title">saveRDS</span>(mCRPC_D,<span class="hljs-string">&quot;mCRPC_D.rds&quot;</span>)<br> <br><span class="hljs-type">GDCdownload</span>(query = <span class="hljs-type">PRAD_D</span>)<br><span class="hljs-type">GDCdownload</span>(query = mCRPC_D)<br> <br><span class="hljs-type">PRAD_pre1</span> &lt;- <span class="hljs-type">GDCprepare</span>(query = <span class="hljs-type">PRAD_D</span>, save = <span class="hljs-type">TRUE</span>, save.filename = <span class="hljs-string">&quot;PRAD_pre1.rda&quot;</span>)<br><span class="hljs-title">mCRPC_pre1</span> &lt;- <span class="hljs-type">GDCprepare</span>(query = mCRPC_D, save = <span class="hljs-type">TRUE</span>, save.filename = <span class="hljs-string">&quot;mCRPC_pre1.rda&quot;</span>)<br> <br><span class="hljs-meta"># 导出counts矩阵</span><br><span class="hljs-meta"># PRAD_pre &lt;- PRAD_pre1@assays@data$`HTSeq - Counts`</span><br><span class="hljs-meta"># colnames(PRAD_pre) &lt;- PRAD_pre1@colData@rownames</span><br><br> <br><span class="hljs-meta"># mCRPC_pre &lt;- mCRPC_pre1@assays@data$`HTSeq - Counts`</span><br><span class="hljs-meta"># colnames(mCRPC_pre) &lt;- mCRPC_pre1@colData@rownames</span><br><br><span class="hljs-meta"># library(Matrix)</span><br><span class="hljs-meta"># library(Seurat)</span><br><span class="hljs-meta"># library(plyr)</span><br><span class="hljs-meta"># library(dplyr)</span><br><span class="hljs-meta"># library(patchwork)</span><br><span class="hljs-meta"># library(purrr)</span><br><br></code></pre></td></tr></table></figure>

<ul>
<li>GEO</li>
</ul>
<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br></pre></td><td class="code"><pre><code class="hljs stylus">f_intersect &lt;- <span class="hljs-built_in">function</span>(lc_ol, t_low=<span class="hljs-number">1</span>)&#123;<br>    com_gene &lt;- <span class="hljs-built_in">Reduce</span>(intersect,<span class="hljs-built_in">lapply</span>(lc_ol, rownames))<br>    com_gene &lt;- com_gene<span class="hljs-selector-attr">[com_gene != <span class="hljs-string">&quot;&quot;</span>]</span><br>    res = NULL<br>    res_g &lt;- NULL<br>    <span class="hljs-built_in">for</span>(<span class="hljs-selector-tag">i</span> <span class="hljs-keyword">in</span> <span class="hljs-number">1</span>:<span class="hljs-built_in">length</span>(lc_ol))&#123;<br>        res &lt;- <span class="hljs-built_in">cbind</span>(res, lc_ol<span class="hljs-selector-attr">[[i]</span>]<span class="hljs-selector-attr">[com_gene,]</span>)<br>        res_g  &lt;- <span class="hljs-built_in">c</span>(res_g, <span class="hljs-built_in">rep</span>(<span class="hljs-built_in">names</span>(lc_ol)<span class="hljs-selector-attr">[i]</span>, <span class="hljs-built_in">ncol</span>(lc_ol<span class="hljs-selector-attr">[[i]</span>])))<br>    &#125;<br>    res &lt;- res<span class="hljs-selector-attr">[rowMeans(res) &gt; t_low,]</span><br>    <span class="hljs-built_in">list</span>(c=res, g=res_g)<br>&#125;<br><br>f_intersect_mg &lt;- <span class="hljs-built_in">function</span>(lc_glN, lc_gln)&#123;<br>    res &lt;- NULL<br>    <span class="hljs-keyword">for</span> (<span class="hljs-selector-tag">i</span> <span class="hljs-keyword">in</span> <span class="hljs-number">1</span>:<span class="hljs-built_in">length</span>(lc_glN))&#123;<br>        res  &lt;- <span class="hljs-built_in">c</span>(res, <span class="hljs-built_in">rep</span>(lc_glN<span class="hljs-selector-attr">[i]</span>, lc_gln<span class="hljs-selector-attr">[i]</span>))<br>    &#125;<br>    res<br>&#125;<br><br>f_intersect_g &lt;- <span class="hljs-built_in">function</span>(lc_counts, lc_ctN, lc_ctn, lc_trN)&#123;<br>    <span class="hljs-built_in">c</span>(<span class="hljs-built_in">rep</span>(lc_ctN, lc_ctn), <span class="hljs-built_in">rep</span>(lc_trN, <span class="hljs-built_in">ncol</span>(lc_counts)-lc_ctn))<br>&#125;<br><br>f_intersect_c &lt;- <span class="hljs-built_in">function</span>(lc_g)&#123;<br>    <span class="hljs-built_in">paste</span>(lc_g,<span class="hljs-number">1</span>:<span class="hljs-built_in">length</span>(lc_g),sep=<span class="hljs-string">&#x27;&#x27;</span>)<br>&#125;<br><br>f_intersect_r &lt;- <span class="hljs-built_in">function</span>(lc_d, lc_s, lc_e, lc_sub=F)&#123;<br>    lc_s = <span class="hljs-built_in">which</span>(<span class="hljs-built_in">colnames</span>(lc_d) == lc_s)<br>    lc_e = <span class="hljs-built_in">which</span>(<span class="hljs-built_in">colnames</span>(lc_d) == lc_e)<br>    <span class="hljs-built_in">if</span>(lc_sub)&#123;<br>        <span class="hljs-built_in">return</span>(lc_d<span class="hljs-selector-attr">[,-(lc_s:lc_e)]</span>)<br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>        <span class="hljs-built_in">return</span>(lc_d<span class="hljs-selector-attr">[,(lc_s:lc_e)]</span>)<br>    &#125;<br>&#125;<br><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br></pre></td><td class="code"><pre><code class="hljs stylus">f_id2name &lt;- <span class="hljs-built_in">function</span>(lc_exp, lc_db)&#123;<br>    <span class="hljs-built_in">if</span>(!is<span class="hljs-selector-class">.data</span><span class="hljs-selector-class">.frame</span>(lc_db))&#123;<br>        lc_ids &lt;- <span class="hljs-built_in">toTable</span>(lc_db)<br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>        lc_ids &lt;- lc_db<br>    &#125;<br>    res &lt;- lc_exp<span class="hljs-selector-attr">[rownames(lc_exp) %in% lc_ids[[1]</span>],]<br>    lc_ids=lc_ids<span class="hljs-selector-attr">[match(rownames(res),lc_ids[[1]</span>]),]<br>    lc_tmp = <span class="hljs-built_in">by</span>(res,<br>         lc_ids<span class="hljs-selector-attr">[[2]</span>],<br>         <span class="hljs-built_in">function</span>(x) <span class="hljs-built_in">rownames</span>(x)<span class="hljs-selector-attr">[which.max(rowMeans(x))]</span>)<br>    lc_probes = as<span class="hljs-selector-class">.character</span>(lc_tmp)<br>    res = res<span class="hljs-selector-attr">[rownames(res) %in% lc_probes,]</span><br>    <span class="hljs-built_in">rownames</span>(res)=lc_ids<span class="hljs-selector-attr">[match(rownames(res),lc_ids[[1]</span>]),<span class="hljs-number">2</span>]<br>    res<br>&#125;<br><br><span class="hljs-function"><span class="hljs-title">library</span><span class="hljs-params">(GEOquery)</span></span><br>f_getGPL &lt;- <span class="hljs-built_in">function</span>(lc_GPLN, lc_local = F)&#123;<br>    <span class="hljs-built_in">options</span>(stringsAsFactors = F)<br>    <span class="hljs-keyword">if</span> (!file<span class="hljs-selector-class">.exists</span>(lc_GPLN))&#123;dir<span class="hljs-selector-class">.create</span>(lc_GPLN)&#125;<br>    <span class="hljs-built_in">if</span>(lc_local)&#123;<br>        gpl=read<span class="hljs-selector-class">.table</span>(file<span class="hljs-selector-class">.path</span>(lc_GPLN, lc_GPLN),<br>               <span class="hljs-selector-tag">header</span> = TRUE,fill = T,sep = <span class="hljs-string">&quot;\t&quot;</span>,<br>               comment<span class="hljs-selector-class">.char</span> = <span class="hljs-string">&quot;#&quot;</span>,<br>               stringsAsFactors = FALSE,<br>               <span class="hljs-selector-tag">quote</span> = <span class="hljs-string">&quot;&quot;</span>)<br>        <span class="hljs-built_in">return</span>(gpl)<br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>        <span class="hljs-built_in">return</span>(<span class="hljs-built_in">Table</span>(<span class="hljs-built_in">getGEO</span>(lc_GPLN,destdir = lc_GPLN)))<br>    &#125;<br>&#125;<br><br>f_getGEO &lt;- <span class="hljs-built_in">function</span>(lc_GEOID, lc_GPLN)&#123;<br>    <span class="hljs-keyword">if</span> (!file<span class="hljs-selector-class">.exists</span>(lc_GEOID))&#123;dir<span class="hljs-selector-class">.create</span>(lc_GEOID)&#125;<br>    gset &lt;- <span class="hljs-built_in">getGEO</span>(lc_GEOID, GSEMatrix =TRUE, AnnotGPL=F, destdir=lc_GEOID)<br>    <span class="hljs-keyword">if</span> (<span class="hljs-built_in">length</span>(gset) &gt; <span class="hljs-number">1</span>) idx &lt;- <span class="hljs-built_in">grep</span>(lc_GPLN, <span class="hljs-built_in">attr</span>(gset, <span class="hljs-string">&quot;names&quot;</span>)) <span class="hljs-keyword">else</span> idx &lt;- <span class="hljs-number">1</span><br>    gset &lt;- gset<span class="hljs-selector-attr">[[idx]</span>]<br>    <span class="hljs-built_in">fvarLabels</span>(gset) &lt;- make<span class="hljs-selector-class">.names</span>(<span class="hljs-built_in">fvarLabels</span>(gset))<br>    <span class="hljs-built_in">exprs</span>(gset)<br>&#125;<br><br></code></pre></td></tr></table></figure>

<figure class="highlight clean"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br></pre></td><td class="code"><pre><code class="hljs clean">GSE70768 &lt;- f_getGEO(<span class="hljs-string">&quot;GSE70768&quot;</span>, <span class="hljs-string">&quot;GPL10558&quot;</span>)<br>GPL10558 = f_getGPL(<span class="hljs-string">&#x27;GPL10558&#x27;</span>)[,c(<span class="hljs-string">&#x27;ID&#x27;</span>,<span class="hljs-string">&#x27;Symbol&#x27;</span>)]<br>GSE70768 &lt;- f_id2name(GSE70768, GPL10558)<br># GSE70768 &lt;- <span class="hljs-number">2</span>^GSE70768 # log2 transformed and quantile normalized<br># GSE70768_CRPC &lt;-  CreateSeuratObject(counts = GSE70768, project = <span class="hljs-string">&quot;GSE70768_CRPC&quot;</span>) <br># GSE70768_CRPC[[<span class="hljs-string">&#x27;group&#x27;</span>]] &lt;- <span class="hljs-string">&#x27;CRPC&#x27;</span><br><br>GPL15659 &lt;- f_getGPL(<span class="hljs-string">&#x27;GPL15659&#x27;</span>)[,c(<span class="hljs-string">&#x27;ID&#x27;</span>,<span class="hljs-string">&#x27;GENE_SYMBOL&#x27;</span>)]<br>GSE74367 &lt;-  f_getGEO(<span class="hljs-string">&quot;GSE74367&quot;</span>, <span class="hljs-string">&quot;GPL15659&quot;</span>)<br>GSE74367 &lt;- f_id2name(GSE74367, GPL15659)<br># GSE74367 &lt;- <span class="hljs-number">2</span>^GSE74367 # batch-normalized log2 Cy3 signal intensity<br># GSE74367_CRPC &lt;-  CreateSeuratObject(counts = GSE74367, project = <span class="hljs-string">&quot;GSE74367_CRPC&quot;</span>) <br># GSE74367_CRPC[[<span class="hljs-string">&#x27;group&#x27;</span>]] &lt;- <span class="hljs-string">&#x27;CRPC&#x27;</span><br><br>GSE101607 &lt;- f_getGEO(<span class="hljs-string">&quot;GSE101607&quot;</span>, <span class="hljs-string">&quot;GPL10558&quot;</span>)<br>GSE101607 &lt;- f_id2name(GSE101607, GPL10558)<br># GSE101607_CRPC &lt;-  CreateSeuratObject(counts = GSE101607, project = <span class="hljs-string">&quot;GSE101607_CRPC&quot;</span>) <br># GSE101607_CRPC[[<span class="hljs-string">&#x27;group&#x27;</span>]] &lt;- <span class="hljs-string">&#x27;CRPC&#x27;</span><br><br></code></pre></td></tr></table></figure>

<h2 id="第二步-整合数据"><a href="#第二步-整合数据" class="headerlink" title="第二步 整合数据"></a>第二步 整合数据</h2><figure class="highlight autoit"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br></pre></td><td class="code"><pre><code class="hljs autoit">f_tcga_fpkm &lt;- function(lc_pre1, lc_exons_gene_lens)&#123;<br>    lc_pre1_l &lt;- lc_exons_gene_lens[lc_pre1<span class="hljs-symbol">@rowRanges</span>$ensembl_gene_id,]/<span class="hljs-number">1000</span> <span class="hljs-meta"># 转kb</span><br>    lc_pre1_rpk &lt;- lc_pre1<span class="hljs-symbol">@assays</span><span class="hljs-symbol">@data</span>$`HTSeq - Counts`/lc_pre1_l<br>    lc_pre1_fpkm &lt;- t(t(lc_pre1_rpk)/colSums(lc_pre1<span class="hljs-symbol">@assays</span><span class="hljs-symbol">@data</span>$`HTSeq - Counts`) * <span class="hljs-number">10</span>^<span class="hljs-number">6</span>)<br>    lc_pre1_fpkm<br>    colnames(lc_pre1_fpkm) &lt;- lc_pre1<span class="hljs-symbol">@colData</span><span class="hljs-symbol">@rownames</span><br>    rownames(lc_pre1_fpkm) &lt;- lc_pre1<span class="hljs-symbol">@rowRanges</span>$external_gene_name<br>    lc_pre1_fpkm<br>&#125;<br>f_tcga_row &lt;- function(lc_pre1)&#123;<br>    lc_counts &lt;- lc_pre1<span class="hljs-symbol">@assays</span><span class="hljs-symbol">@data</span>$`HTSeq - Counts`<br>    colnames(lc_counts) &lt;- lc_pre1<span class="hljs-symbol">@colData</span><span class="hljs-symbol">@rownames</span><br>    rownames(lc_counts) &lt;- lc_pre1<span class="hljs-symbol">@rowRanges</span>$external_gene_name<br>    lc_counts<br>&#125;<br>fpkmToTpm &lt;- function(fpkm)&#123;<br>    <span class="hljs-built_in">exp</span>(<span class="hljs-built_in">log</span>(fpkm) - <span class="hljs-built_in">log</span>(sum(fpkm)) + <span class="hljs-built_in">log</span>(<span class="hljs-number">1e6</span>))<br>&#125;<br>f_fpkmToTpm &lt;- function(l_e)&#123;<br>     apply(l_e,<span class="hljs-number">2</span>,fpkmToTpm)<br>&#125;<br>f_tcga_getSampleID &lt;- function(lc_pre1)&#123;<br>    cn &lt;- lc_pre1<span class="hljs-symbol">@colData</span><span class="hljs-symbol">@rownames</span><br>    cn &lt;- unlist(t(data.frame(strsplit(a, <span class="hljs-string">&quot;-&quot;</span>))[<span class="hljs-number">4</span>,])[,<span class="hljs-number">1</span>])<br>    names(cn) &lt;- <span class="hljs-literal">NULL</span><br>    substr(cn,<span class="hljs-number">1</span>,<span class="hljs-number">2</span>)<br>&#125;<br></code></pre></td></tr></table></figure>

<figure class="highlight subunit"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs subunit"># https://api.gdc.cancer.gov/data/25aa497c-e615<span class="hljs-string">-4</span>cb7<span class="hljs-string">-8751</span><span class="hljs-string">-71</span>f744f9691f<br></code></pre></td></tr></table></figure>

<p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/10/image-1.png"><img src="https://img-cdn.limour.top/blog_wp/2021/10/image-1.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
<p>下载解压</p>
<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">library</span><span class="hljs-params">(GenomicFeatures)</span></span><br>txdb &lt;- <span class="hljs-built_in">makeTxDbFromGFF</span>(<span class="hljs-string">&quot;gencode.v22.annotation.gtf&quot;</span>,format=<span class="hljs-string">&quot;gtf&quot;</span>)<br>exons_gene &lt;- <span class="hljs-built_in">exonsBy</span>(txdb, by = <span class="hljs-string">&quot;gene&quot;</span>)<br>exons_gene_lens &lt;- <span class="hljs-built_in">lapply</span>(exons_gene,<span class="hljs-built_in">function</span>(x)&#123;<span class="hljs-built_in">sum</span>(<span class="hljs-attribute">width</span>(<span class="hljs-built_in">reduce</span>(x)))&#125;)<br>exons_gene_lens1 &lt;- as<span class="hljs-selector-class">.data</span><span class="hljs-selector-class">.frame</span>(exons_gene_lens)<br>exons_gene_lens1 &lt;- <span class="hljs-built_in">t</span>(exons_gene_lens1)<br>exons_gene_lens1 &lt;- as<span class="hljs-selector-class">.data</span><span class="hljs-selector-class">.frame</span>(exons_gene_lens1)<br><span class="hljs-function"><span class="hljs-title">rownames</span><span class="hljs-params">(exons_gene_lens1)</span></span> &lt;- <span class="hljs-built_in">gsub</span>(<span class="hljs-string">&quot;\\.(\\.?\\d*)&quot;</span>,<span class="hljs-string">&quot;&quot;</span>,<span class="hljs-built_in">rownames</span>(exons_gene_lens1))<br><span class="hljs-function"><span class="hljs-title">saveRDS</span><span class="hljs-params">(exons_gene_lens1,<span class="hljs-string">&#x27;exons_gene_lens.rds&#x27;</span>)</span></span><br></code></pre></td></tr></table></figure>

<figure class="highlight haskell"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br></pre></td><td class="code"><pre><code class="hljs haskell"><span class="hljs-title">sym2id</span>.db &lt;- <span class="hljs-class"><span class="hljs-keyword">data</span>.frame(<span class="hljs-title">sym</span>=<span class="hljs-type">PRAD_pre1</span>@<span class="hljs-title">rowRanges</span>$<span class="hljs-title">external_gene_name</span>, <span class="hljs-type">ID</span>=<span class="hljs-type">PRAD_pre1</span>@<span class="hljs-title">rowRanges</span>$<span class="hljs-title">ensembl_gene_id</span>)</span><br><span class="hljs-title">saveRDS</span>(sym2id.db,&#x27;sym2id.db&#x27;)<br><span class="hljs-title">f_GEO2fpkm</span> &lt;- function(lc_exp, lc_exons_gene_lens)&#123;<br>        lc_pre1_l &lt;- lc_exons_gene_lens[rownames(lc_exp),]/<span class="hljs-number">1000</span> # 转kb<br>        lc_pre1_rpk &lt;-lc_exp/lc_pre1_l<br>        lc_pre1_fpkm &lt;- t(t(lc_pre1_rpk)/colSums(lc_exp) * <span class="hljs-number">10</span>^<span class="hljs-number">6</span>)<br>        lc_pre1_fpkm<br>&#125;<br></code></pre></td></tr></table></figure>

<figure class="highlight subunit"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs subunit"># PRAD_pre &lt;- f_intersect_sub(PRAD_pre, c(&#x27;TCGA-HC<span class="hljs-string">-8265</span><span class="hljs-string">-01</span>B<span class="hljs-string">-04</span>R<span class="hljs-string">-2302</span><span class="hljs-string">-07</span>&#x27;,&#x27;TCGA-HC<span class="hljs-string">-8258</span><span class="hljs-string">-01</span>B<span class="hljs-string">-05</span>R<span class="hljs-string">-2302</span><span class="hljs-string">-07</span>&#x27;, &#x27;TCGA-HC<span class="hljs-string">-7740</span><span class="hljs-string">-01</span>B<span class="hljs-string">-04</span>R<span class="hljs-string">-2302</span><span class="hljs-string">-07</span>&#x27;))<br>GSE101607 &lt;- f_log2(GSE101607)<br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br></pre></td><td class="code"><pre><code class="hljs stylus">tcga &lt;- <span class="hljs-built_in">f_intersect</span>(<span class="hljs-built_in">list</span>(tcga_PRAD=<span class="hljs-built_in">f_tcga_row</span>(PRAD_pre1), tcga_mCRPC=<span class="hljs-built_in">f_tcga_row</span>(mCRPC_pre1)))<br><br>GSE70768_CRPC &lt;- GSE70768<span class="hljs-selector-attr">[,1:13]</span><br>GSE70768_PRAD &lt;- <span class="hljs-built_in">f_intersect_r</span>(GSE70768, <span class="hljs-string">&#x27;GSM1817720&#x27;</span>, <span class="hljs-string">&#x27;GSM1817832&#x27;</span>)<br><br>GSE74367_CRPC &lt;- GSE74367<span class="hljs-selector-attr">[,21:65]</span><br>GSE74367_PRAD &lt;- <span class="hljs-built_in">f_intersect_r</span>(GSE74367, <span class="hljs-string">&#x27;GSM1918981&#x27;</span>, <span class="hljs-string">&#x27;GSM1918991&#x27;</span>)<br><br>GSE101607_CRPC &lt;- GSE101607<span class="hljs-selector-attr">[,1:40]</span><br>GSE101607_PRAD1 &lt;- <span class="hljs-built_in">f_intersect_r</span>(GSE101607, <span class="hljs-string">&#x27;GSM2710899&#x27;</span>, <span class="hljs-string">&#x27;GSM2710905&#x27;</span>)<br>GSE101607_PRAD2 &lt;- GSE101607<span class="hljs-selector-attr">[, <span class="hljs-string">&#x27;GSM2710886&#x27;</span>]</span><br>GSE101607_PRAD &lt;- <span class="hljs-built_in">cbind</span>(GSE101607_PRAD2, GSE101607_PRAD1)<br><span class="hljs-function"><span class="hljs-title">colnames</span><span class="hljs-params">(GSE101607_PRAD)</span></span><span class="hljs-selector-attr">[[1]</span>] &lt;- <span class="hljs-string">&#x27;GSM2710886&#x27;</span><br><br>GSE28403_CRPC &lt;- <span class="hljs-built_in">f_intersect_sub</span>(GSE28403, <span class="hljs-built_in">c</span>(<span class="hljs-string">&#x27;GSM701959&#x27;</span>,<span class="hljs-string">&#x27;GSM701961&#x27;</span>, <span class="hljs-string">&#x27;GSM701962&#x27;</span>, <span class="hljs-string">&#x27;GSM701963&#x27;</span>))<br>GSE28403_PRAD &lt;- GSE28403<span class="hljs-selector-attr">[, c(<span class="hljs-string">&#x27;GSM701959&#x27;</span>,<span class="hljs-string">&#x27;GSM701961&#x27;</span>, <span class="hljs-string">&#x27;GSM701962&#x27;</span>, <span class="hljs-string">&#x27;GSM701963&#x27;</span>)]</span><br><br></code></pre></td></tr></table></figure>

<h2 id="第三步-批次效应"><a href="#第三步-批次效应" class="headerlink" title="第三步 批次效应"></a>第三步 批次效应</h2><figure class="highlight reasonml"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br><span class="line">66</span><br><span class="line">67</span><br><span class="line">68</span><br><span class="line">69</span><br><span class="line">70</span><br><span class="line">71</span><br><span class="line">72</span><br><span class="line">73</span><br><span class="line">74</span><br><span class="line">75</span><br><span class="line">76</span><br><span class="line">77</span><br><span class="line">78</span><br><span class="line">79</span><br><span class="line">80</span><br><span class="line">81</span><br><span class="line">82</span><br><span class="line">83</span><br><span class="line">84</span><br><span class="line">85</span><br><span class="line">86</span><br><span class="line">87</span><br><span class="line">88</span><br><span class="line">89</span><br><span class="line">90</span><br><span class="line">91</span><br></pre></td><td class="code"><pre><code class="hljs reasonml">f_pca &lt;- <span class="hljs-keyword">function</span>(lc_counts, lc_g)&#123;<br>    res &lt;- prcomp(lc_counts)<br>    res &lt;- data.frame(res$rotation, g = lc_g)<br>    res$CB &lt;- rownames(res)<br>    res<br>&#125;<br><br>library(ggplot2)<br>library(tidyverse)<br>f_pca_p &lt;- <span class="hljs-keyword">function</span>(lc_pca, x=&#x27;PC1&#x27;, y=&#x27;PC2&#x27;)&#123;<br>    ggplot(lc_pca,aes(x=!!sym(x),y=!!sym(y),color=g))+<br>    geom<span class="hljs-constructor">_point()</span>+<br>    theme<span class="hljs-constructor">_bw()</span>+<br>    theme(panel.border=element<span class="hljs-constructor">_blank()</span>,panel.grid.major=element<span class="hljs-constructor">_blank()</span>,<br>          panel.grid.minor=element<span class="hljs-constructor">_blank()</span>,axis.line= element<span class="hljs-constructor">_line(<span class="hljs-params">colour</span> = <span class="hljs-string">&quot;blue&quot;</span>)</span>)<br>&#125;<br><br>library(umap)<br>f_umap &lt;- <span class="hljs-keyword">function</span>(lc_pca,dims=<span class="hljs-number">1</span>:<span class="hljs-number">30</span>)&#123;<br>    res &lt;- umap(lc_pca<span class="hljs-literal">[,<span class="hljs-identifier">dims</span>]</span>)<br>    res &lt;- data.frame(res$layout)<br>    colnames(res) &lt;- c(&#x27;UMAP1&#x27;, &#x27;UMAP2&#x27;)<br>    res$CB &lt;- rownames(res)<br>    tp &lt;- lc_pca<span class="hljs-literal">[,<span class="hljs-identifier">c</span>(&#x27;<span class="hljs-identifier">g</span>&#x27;,&#x27;CB&#x27;)]</span><br>    res &lt;- merge(res, tp, by=<span class="hljs-string">&quot;CB&quot;</span>)<br>    res<br>&#125;<br>f_umap_p &lt;- <span class="hljs-keyword">function</span>(lc_umap)&#123;<br>    ggplot(lc_umap,aes(x=UMAP1,y=UMAP2,color=g))+<br>    geom<span class="hljs-constructor">_point()</span>+<br>    theme<span class="hljs-constructor">_bw()</span>+<br>    theme(panel.border=element<span class="hljs-constructor">_blank()</span>,panel.grid.major=element<span class="hljs-constructor">_blank()</span>,<br>          panel.grid.minor=element<span class="hljs-constructor">_blank()</span>,axis.line= element<span class="hljs-constructor">_line(<span class="hljs-params">colour</span> = <span class="hljs-string">&quot;blue&quot;</span>)</span>)<br>&#125;<br><br>library(ggplot2)<br>library(reshape2)<br>library(plyr)<br>library(dplyr)<br>library(patchwork)<br>library(purrr)<br> <br>f_gl_boxp &lt;- <span class="hljs-keyword">function</span>(lc_exp, lc_g, lc_delta_ylim)&#123;<br>    lc_exp_L = melt(lc_exp)<br>    colnames(lc_exp_L) = c(&#x27;symbol<span class="hljs-character">&#x27;,&#x27;</span>sample<span class="hljs-character">&#x27;,&#x27;</span>value&#x27;)<br>    lc_exp_L$group = lc_g<br>    p=ggplot(lc_exp_L,aes(x=sample,y=value,fill=group))+geom<span class="hljs-constructor">_boxplot(<span class="hljs-params">outlier</span>.<span class="hljs-params">shape</span> = NA)</span><br>    p=p+theme<span class="hljs-constructor">_set(<span class="hljs-params">theme_set</span>(<span class="hljs-params">theme_bw</span>(<span class="hljs-params">base_size</span>=20)</span>))<br>    p=p+theme(text=element<span class="hljs-constructor">_text(<span class="hljs-params">face</span>=&#x27;<span class="hljs-params">bold</span>&#x27;)</span>,axis.text.x=element<span class="hljs-constructor">_text(<span class="hljs-params">angle</span>=30,<span class="hljs-params">hjust</span>=1)</span>,axis.title=element<span class="hljs-constructor">_blank()</span>)<br>    lc_ylim = unlist(by(lc_exp_L,<br>     lc_exp_L$sample,<br>     <span class="hljs-keyword">function</span>(x)&#123;boxplot.stats(x$value)$stats<span class="hljs-literal">[<span class="hljs-identifier">c</span>(<span class="hljs-number">1</span>, <span class="hljs-number">5</span>)]</span>&#125;))<br>    lc_ylim &lt;- c(min(lc_ylim), max(lc_ylim)) + lc_delta_ylim<br>    p=p + coord<span class="hljs-constructor">_cartesian(<span class="hljs-params">ylim</span> = <span class="hljs-params">lc_ylim</span>)</span><br>    p<br>&#125;<br> <br>f_icg_boxp &lt;- <span class="hljs-keyword">function</span>(lc_exp, lc_icg, lc_g)&#123;<br>    lc_exp_L = melt(lc_exp<span class="hljs-literal">[<span class="hljs-identifier">lc_icg</span>,]</span>)<br>    lc_exp_L &lt;- cbind(lc_exp_L, rownames(lc_exp_L))<br>    colnames(lc_exp_L)=c(&#x27;value<span class="hljs-character">&#x27;,&#x27;</span>sample&#x27;)<br>    lc_exp_L$group = lc_g<br>    p=ggplot(lc_exp_L,aes(x=group,y=value,fill=group))+geom<span class="hljs-constructor">_boxplot()</span><br>    p=p+stat<span class="hljs-constructor">_summary(<span class="hljs-params">fun</span>=<span class="hljs-string">&quot;mean&quot;</span>,<span class="hljs-params">geom</span>=<span class="hljs-string">&quot;point&quot;</span>,<span class="hljs-params">shape</span>=23,<span class="hljs-params">size</span>=3,<span class="hljs-params">fill</span>=<span class="hljs-string">&quot;red&quot;</span>)</span><br>    p=p+theme<span class="hljs-constructor">_set(<span class="hljs-params">theme_set</span>(<span class="hljs-params">theme_bw</span>(<span class="hljs-params">base_size</span>=20)</span>))<br>    p=p+theme(text=element<span class="hljs-constructor">_text(<span class="hljs-params">face</span>=&#x27;<span class="hljs-params">bold</span>&#x27;)</span>,axis.text.x=element<span class="hljs-constructor">_text(<span class="hljs-params">angle</span>=30,<span class="hljs-params">hjust</span>=1)</span>,axis.title=element<span class="hljs-constructor">_blank()</span>)<br>    p=p+ggtitle(lc_icg)+theme(plot.title = element<span class="hljs-constructor">_text(<span class="hljs-params">hjust</span> = 0.5)</span>)<br>    p<br>&#125;<br><br># 若缺少sva包，则安装<br># options(BioC_mirror=<span class="hljs-string">&quot;https://mirrors.tuna.tsinghua.edu.cn/bioconductor&quot;</span>)<br># BiocManager::install(<span class="hljs-string">&quot;sva&quot;</span>, update=F)<br>library(sva)<br>library(limma)<br>f_removeBE &lt;- <span class="hljs-keyword">function</span>(lc_dat, lc_batch, lc_g, use_ComBat=F)&#123;<br>    <span class="hljs-keyword">if</span>(use_ComBat)&#123;<br>        lc_mod &lt;- model.matrix(~<span class="hljs-keyword">as</span>.factor(lc_g))<br>        res &lt;- <span class="hljs-constructor">ComBat(<span class="hljs-params">dat</span> = <span class="hljs-params">lc_dat</span>, <span class="hljs-params">batch</span> = <span class="hljs-params">as</span>.<span class="hljs-params">factor</span>(<span class="hljs-params">lc_batch</span>)</span>, <span class="hljs-keyword">mod</span> = lc_mod)<br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>        lc_mod &lt;- model.matrix(~<span class="hljs-number">0</span>+<span class="hljs-keyword">as</span>.factor(lc_g))<br>        res &lt;- remove<span class="hljs-constructor">BatchEffect(<span class="hljs-params">lc_dat</span>, <span class="hljs-params">batch</span> = <span class="hljs-params">as</span>.<span class="hljs-params">factor</span>(<span class="hljs-params">lc_batch</span>)</span>, design = lc_mod)<br>    &#125;<br>    res<br>&#125;<br><br>library(ggdendro)<br>f_DEG_hclust &lt;- <span class="hljs-keyword">function</span>(lc_counts)&#123;<br>    ggdendrogram(hclust(dist(t(lc_counts))), rotate = T, size = <span class="hljs-number">3</span>)+theme(axis.text = element<span class="hljs-constructor">_text(<span class="hljs-params">size</span>=14,<span class="hljs-params">face</span> = <span class="hljs-string">&quot;bold&quot;</span>)</span>)<br>&#125;<br><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br></pre></td><td class="code"><pre><code class="hljs stylus">gse<span class="hljs-variable">$m</span> &lt;- <span class="hljs-built_in">f_removeBE</span>(gse<span class="hljs-variable">$c</span>, gse<span class="hljs-variable">$b</span>, gse<span class="hljs-variable">$t</span>, use_ComBat = T)<br><span class="hljs-function"><span class="hljs-title">f_icg_boxp</span><span class="hljs-params">(gse<span class="hljs-variable">$m</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, gse<span class="hljs-variable">$t</span>)</span></span><br><span class="hljs-function"><span class="hljs-title">f_icg_boxp</span><span class="hljs-params">(normalizeBetweenArrays(cbind(GSE74367_PRAD,GSE74367_CRPC)</span></span>),<span class="hljs-string">&#x27;GAPDH&#x27;</span>,<br>           <span class="hljs-built_in">f_intersect_mg</span>(<span class="hljs-built_in">c</span>(<span class="hljs-string">&#x27;PRAD&#x27;</span>, <span class="hljs-string">&#x27;CRPC&#x27;</span>),<span class="hljs-built_in">c</span>(<span class="hljs-built_in">ncol</span>(GSE74367_PRAD),<span class="hljs-built_in">ncol</span>(GSE74367_CRPC))))<br><span class="hljs-function"><span class="hljs-title">f_icg_boxp</span><span class="hljs-params">(normalizeBetweenArrays(gse<span class="hljs-variable">$m</span>)</span></span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, gse<span class="hljs-variable">$t</span>)<br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">10</span>, repr.plot.height=<span class="hljs-number">10</span>)</span></span><br>(<span class="hljs-built_in">f_icg_boxp</span>(gse<span class="hljs-variable">$c</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, gse<span class="hljs-variable">$g</span>) + <span class="hljs-built_in">f_icg_boxp</span>(gse<span class="hljs-variable">$m</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, gse<span class="hljs-variable">$g</span>))/<br>(<span class="hljs-built_in">f_icg_boxp</span>(gse<span class="hljs-variable">$c</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, gse<span class="hljs-variable">$t</span>) + <span class="hljs-built_in">f_icg_boxp</span>(gse<span class="hljs-variable">$m</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, gse<span class="hljs-variable">$t</span>))<br>(<span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(gse<span class="hljs-variable">$c</span>,gse<span class="hljs-variable">$g</span>)) + <span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(gse<span class="hljs-variable">$m</span>,gse<span class="hljs-variable">$g</span>)))/<br>(<span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(gse<span class="hljs-variable">$c</span>,gse<span class="hljs-variable">$t</span>)) + <span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(gse<span class="hljs-variable">$m</span>,gse<span class="hljs-variable">$t</span>)))<br>(<span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(gse<span class="hljs-variable">$c</span>,gse<span class="hljs-variable">$g</span>))) + <span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(gse<span class="hljs-variable">$m</span>,gse<span class="hljs-variable">$g</span>))))/<br>(<span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(gse<span class="hljs-variable">$c</span>,gse<span class="hljs-variable">$t</span>))) + <span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(gse<span class="hljs-variable">$m</span>,gse<span class="hljs-variable">$t</span>))))<br></code></pre></td></tr></table></figure>

<h2 id="第四步-计算DEGs"><a href="#第四步-计算DEGs" class="headerlink" title="第四步 计算DEGs"></a>第四步 计算DEGs</h2><figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">library</span><span class="hljs-params">(limma)</span></span><br><span class="hljs-function"><span class="hljs-title">library</span><span class="hljs-params">(pheatmap)</span></span><br>f_getDEG &lt;- <span class="hljs-built_in">function</span>(lc_counts, lc_group_list, lc_contrasts)&#123;<br>    <span class="hljs-keyword">if</span> (<span class="hljs-built_in">length</span>(lc_contrasts) == <span class="hljs-number">2</span>)&#123;lc_contrasts = <span class="hljs-built_in">paste0</span>(lc_contrasts,collapse = <span class="hljs-string">&quot;-&quot;</span>)&#125;<br>    lc_design &lt;- model<span class="hljs-selector-class">.matrix</span>(~<span class="hljs-number">0</span>+<span class="hljs-built_in">factor</span>(lc_group_list))<br>    <span class="hljs-built_in">colnames</span>(lc_design) &lt;- <span class="hljs-built_in">levels</span>(<span class="hljs-built_in">factor</span>(lc_group_list))<br>    <span class="hljs-built_in">rownames</span>(lc_design) &lt;- <span class="hljs-built_in">colnames</span>(lc_counts)<br>    lc_fit &lt;- <span class="hljs-built_in">lmFit</span>(lc_counts, lc_design)<br>    lc_cont<span class="hljs-selector-class">.matrix</span> &lt;- <span class="hljs-built_in">makeContrasts</span>(contrasts=lc_contrasts, levels=lc_design)<br>    <span class="hljs-built_in">print</span>(lc_cont.matrix)<br>    lc_fit2 &lt;- contrasts<span class="hljs-selector-class">.fit</span>(lc_fit, lc_cont.matrix)<br>    lc_fit2 &lt;- <span class="hljs-built_in">eBayes</span>(lc_fit2, <span class="hljs-number">0.01</span>)<br>    <span class="hljs-built_in">topTable</span>(lc_fit2, adjust=<span class="hljs-string">&quot;fdr&quot;</span>, sort.by=<span class="hljs-string">&quot;B&quot;</span>, number=Inf)<br>&#125;<br><br><span class="hljs-function"><span class="hljs-title">library</span><span class="hljs-params">(ggplot2)</span></span><br><span class="hljs-function"><span class="hljs-title">library</span><span class="hljs-params">(ggrepel)</span></span><br>f_DEG_Volcano &lt;- <span class="hljs-built_in">function</span>(lc_logFC, lc_p, lc_gene, Threshold_logFC = <span class="hljs-number">1</span>, Threshold_p = <span class="hljs-number">0.05</span>, lc_rep=<span class="hljs-number">1</span>:<span class="hljs-number">10</span>, lc_p_m=<span class="hljs-number">1</span>e-<span class="hljs-number">10</span>)&#123;<br>    col_vector = <span class="hljs-built_in">rep</span>(<span class="hljs-built_in">rgb</span>(<span class="hljs-number">108</span>, <span class="hljs-number">200</span>, <span class="hljs-number">228</span>, maxColorValue = <span class="hljs-number">255</span>), <span class="hljs-built_in">length</span>(lc_logFC))<br>    col_vector<span class="hljs-selector-attr">[lc_p &lt; Threshold_p &amp; lc_logFC &gt; Threshold_logFC]</span> = <span class="hljs-built_in">rgb</span>(<span class="hljs-number">226</span>, <span class="hljs-number">61</span>, <span class="hljs-number">75</span>, maxColorValue = <span class="hljs-number">255</span>)<br>    col_vector<span class="hljs-selector-attr">[lc_p &lt; Threshold_p &amp; lc_logFC &lt; -Threshold_logFC]</span> = <span class="hljs-built_in">rgb</span>(<span class="hljs-number">232</span>, <span class="hljs-number">168</span>, <span class="hljs-number">71</span>, maxColorValue = <span class="hljs-number">255</span>)<br>    lc_p<span class="hljs-selector-attr">[lc_p &lt; lc_p_m]</span> = lc_p_m<br>    lc_p<span class="hljs-selector-attr">[lc_p &gt; 1  is.na(lc_p)]</span> = <span class="hljs-number">1</span><br>    df = data<span class="hljs-selector-class">.frame</span>(logFC &lt;- lc_logFC, `<span class="hljs-built_in">-log10</span>(P)` &lt;- <span class="hljs-built_in">-log10</span>(lc_p), col &lt;- col_vector, gene &lt;- lc_gene)<br>    <span class="hljs-built_in">colnames</span>(df) &lt;- <span class="hljs-built_in">c</span>(<span class="hljs-string">&#x27;logFC&#x27;</span>, <span class="hljs-string">&#x27;-log10(P)&#x27;</span>, <span class="hljs-string">&quot;col&quot;</span>, <span class="hljs-string">&quot;gene&quot;</span>)<br>    lc_tp_logFC &lt;- df<span class="hljs-variable">$logFC</span><br>    lc_tp_logFC<span class="hljs-selector-attr">[lc_p&gt;=Threshold_p]</span> = <span class="hljs-number">0</span><br>    lc_idx &lt;- <span class="hljs-attribute">order</span>(lc_tp_logFC)[<span class="hljs-built_in">c</span>(lc_rep, <span class="hljs-built_in">length</span>(lc_gene)+<span class="hljs-number">1</span>-lc_rep)]<br>    res &lt;- <span class="hljs-built_in">ggplot</span>() + <span class="hljs-built_in">geom_point</span>(<span class="hljs-built_in">aes</span>(logFC, `<span class="hljs-built_in">-log10</span>(P)`, col=<span class="hljs-built_in">I</span>(col)), data = df) <br>    res &lt;- res + <span class="hljs-built_in">theme_bw</span>() + <span class="hljs-built_in">theme</span>(panel.<span class="hljs-attribute">grid</span>=<span class="hljs-built_in">element_line</span>(colour=NA))<br>    res &lt;- res + <span class="hljs-built_in">geom_hline</span>(yintercept=<span class="hljs-built_in">-log10</span>(Threshold_p), linetype=<span class="hljs-string">&quot;longdash&quot;</span>)<br>    res &lt;- res + <span class="hljs-built_in">geom_vline</span>(xintercept=<span class="hljs-built_in">c</span>(Threshold_logFC, -Threshold_logFC), linetype=<span class="hljs-string">&quot;longdash&quot;</span>)<br>    res &lt;- res + <span class="hljs-built_in">geom_text_repel</span>(data=df<span class="hljs-selector-attr">[lc_idx,]</span>,<span class="hljs-built_in">aes</span>(logFC,`<span class="hljs-built_in">-log10</span>(P)`,label=gene), force=T, max.overlaps=Inf)<br>    res<br>&#125;<br><br></code></pre></td></tr></table></figure>

<figure class="highlight reasonml"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br></pre></td><td class="code"><pre><code class="hljs reasonml">library(DESeq2)<br>f_dds &lt;- <span class="hljs-keyword">function</span>(l_counts, lc_g, lc_batch=NULL, t_low=<span class="hljs-number">1</span>)&#123;<br>    lc_cond &lt;- factor(lc_g)<br>    lc_coldata = data.frame(row.names=colnames(l_counts), lc_cond)<br>    <span class="hljs-keyword">if</span>(length(lc_batch) != <span class="hljs-number">0</span> )&#123;<br>        lc_bt &lt;- factor(lc_batch)<br>        lc_dds &lt;- <span class="hljs-constructor">DESeqDataSetFromMatrix(<span class="hljs-params">countData</span> = <span class="hljs-params">l_counts</span>, <span class="hljs-params">colData</span> = <span class="hljs-params">lc_coldata</span>, <span class="hljs-params">design</span>= ~<span class="hljs-params">lc_bt</span> + <span class="hljs-params">lc_cond</span>)</span><br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>        lc_dds &lt;- <span class="hljs-constructor">DESeqDataSetFromMatrix(<span class="hljs-params">countData</span> = <span class="hljs-params">l_counts</span>, <span class="hljs-params">colData</span> = <span class="hljs-params">lc_coldata</span>, <span class="hljs-params">design</span>= ~<span class="hljs-params">lc_cond</span>)</span><br>    &#125;<br>    lc_dds &lt;- lc_dds<span class="hljs-literal">[<span class="hljs-identifier">rowSums</span>(<span class="hljs-identifier">counts</span>(<span class="hljs-identifier">lc_dds</span>))&gt;<span class="hljs-identifier">t_low</span>, ]</span><br>    dds_out &lt;- <span class="hljs-constructor">DESeq(<span class="hljs-params">lc_dds</span>)</span><br>    res &lt;- results(dds_out)<br>    data.frame(res)<br>&#125;<br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">10</span>, repr.plot.height=<span class="hljs-number">10</span>)</span></span><br>gse<span class="hljs-variable">$deg</span> &lt;- <span class="hljs-built_in">f_getDEG</span>(gse<span class="hljs-variable">$m</span>,gse<span class="hljs-variable">$t</span>,<span class="hljs-built_in">c</span>(<span class="hljs-string">&#x27;CRPC&#x27;</span>,<span class="hljs-string">&#x27;PRAD&#x27;</span>))<br><span class="hljs-function"><span class="hljs-title">f_DEG_Volcano</span><span class="hljs-params">(gse<span class="hljs-variable">$deg</span><span class="hljs-variable">$logFC</span>, gse<span class="hljs-variable">$deg</span><span class="hljs-variable">$adj</span>.P.Val, rownames(gse<span class="hljs-variable">$deg</span>)</span></span>, Threshold_logFC = <span class="hljs-number">0.5</span>, lc_p_m = <span class="hljs-number">1</span>e-<span class="hljs-number">30</span>)<br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br></pre></td><td class="code"><pre><code class="hljs stylus">tcga<span class="hljs-variable">$c</span> &lt;- tcga<span class="hljs-variable">$c</span><span class="hljs-selector-attr">[rownames(tcga$c) %in% rownames(gse$m),]</span><br>tcga<span class="hljs-variable">$m</span> &lt;- <span class="hljs-built_in">normalizeBetweenArrays</span>(tcga<span class="hljs-variable">$c</span>)<br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">10</span>, repr.plot.height=<span class="hljs-number">15</span>)</span></span><br>(<span class="hljs-built_in">f_icg_boxp</span>(tcga<span class="hljs-variable">$c</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, tcga<span class="hljs-variable">$g</span>) + <span class="hljs-built_in">f_icg_boxp</span>(tcga<span class="hljs-variable">$m</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, tcga<span class="hljs-variable">$g</span>))/<br>(<span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$c</span>,tcga<span class="hljs-variable">$g</span>)) + <span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$m</span>,tcga<span class="hljs-variable">$g</span>)))/<br>(<span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$c</span>,tcga<span class="hljs-variable">$g</span>))) + <span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$m</span>,tcga<span class="hljs-variable">$g</span>))))<br>tcga<span class="hljs-variable">$pca</span> &lt;- <span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$m</span>,tcga<span class="hljs-variable">$g</span>)<br>tcga<span class="hljs-variable">$t</span> &lt;- tcga<span class="hljs-variable">$g</span><br><span class="hljs-function"><span class="hljs-title">names</span><span class="hljs-params">(tcga<span class="hljs-variable">$t</span>)</span></span> &lt;- <span class="hljs-built_in">colnames</span>(tcga<span class="hljs-variable">$c</span>)<br>tcga<span class="hljs-variable">$pca</span> &lt;- <span class="hljs-built_in">subset</span>(tcga<span class="hljs-variable">$pca</span>, (PC1 &gt; <span class="hljs-number">0.04</span>  PC1 &lt; <span class="hljs-number">0.03</span>)&amp;(PC2 &gt; <span class="hljs-number">0.06</span>  PC2 &lt; <span class="hljs-number">0.01</span>))<br>tcga<span class="hljs-variable">$t</span> &lt;- tcga<span class="hljs-variable">$t</span><span class="hljs-selector-attr">[rownames(tcga$pca)]</span><br><span class="hljs-selector-tag">table</span>(tcga<span class="hljs-variable">$t</span>)<br>tcga<span class="hljs-variable">$m</span> &lt;- tcga<span class="hljs-variable">$m</span><span class="hljs-selector-attr">[,rownames(tcga$pca)]</span><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">10</span>, repr.plot.height=<span class="hljs-number">15</span>)</span></span><br>(<span class="hljs-built_in">f_icg_boxp</span>(tcga<span class="hljs-variable">$c</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, tcga<span class="hljs-variable">$g</span>) + <span class="hljs-built_in">f_icg_boxp</span>(tcga<span class="hljs-variable">$m</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, tcga<span class="hljs-variable">$t</span>))/<br>(<span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$c</span>,tcga<span class="hljs-variable">$g</span>)) + <span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$m</span>,tcga<span class="hljs-variable">$t</span>)))/<br>(<span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$c</span>,tcga<span class="hljs-variable">$g</span>))) + <span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$m</span>,tcga<span class="hljs-variable">$t</span>))))<br>tcga<span class="hljs-variable">$pca</span> &lt;- <span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$m</span>,tcga<span class="hljs-variable">$t</span>)<br>tcga<span class="hljs-variable">$pca</span> &lt;- <span class="hljs-built_in">subset</span>(tcga<span class="hljs-variable">$pca</span>, (PC1 &gt; -<span class="hljs-number">0.03</span> &amp; PC2 &gt;<span class="hljs-number">0.05</span>)  (PC1 &lt; -<span class="hljs-number">0.04</span> &amp; PC2 &lt; <span class="hljs-number">0.03</span>))<br>tcga<span class="hljs-variable">$t</span> &lt;- tcga<span class="hljs-variable">$t</span><span class="hljs-selector-attr">[rownames(tcga$pca)]</span><br><span class="hljs-selector-tag">table</span>(tcga<span class="hljs-variable">$t</span>)<br>tcga<span class="hljs-variable">$m</span> &lt;- tcga<span class="hljs-variable">$m</span><span class="hljs-selector-attr">[,rownames(tcga$pca)]</span><br><span class="hljs-function"><span class="hljs-title">options</span><span class="hljs-params">(repr.plot.width=<span class="hljs-number">10</span>, repr.plot.height=<span class="hljs-number">15</span>)</span></span><br>(<span class="hljs-built_in">f_icg_boxp</span>(tcga<span class="hljs-variable">$c</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, tcga<span class="hljs-variable">$g</span>) + <span class="hljs-built_in">f_icg_boxp</span>(tcga<span class="hljs-variable">$m</span>, <span class="hljs-string">&#x27;GAPDH&#x27;</span>, tcga<span class="hljs-variable">$t</span>))/<br>(<span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$c</span>,tcga<span class="hljs-variable">$g</span>)) + <span class="hljs-built_in">f_pca_p</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$m</span>,tcga<span class="hljs-variable">$t</span>)))/<br>(<span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$c</span>,tcga<span class="hljs-variable">$g</span>))) + <span class="hljs-built_in">f_umap_p</span>(<span class="hljs-built_in">f_umap</span>(<span class="hljs-built_in">f_pca</span>(tcga<span class="hljs-variable">$m</span>,tcga<span class="hljs-variable">$t</span>))))<br><span class="hljs-function"><span class="hljs-title">names</span><span class="hljs-params">(tcga<span class="hljs-variable">$g</span>)</span></span> &lt;- <span class="hljs-built_in">colnames</span>(tcga<span class="hljs-variable">$c</span>)<br>tcga<span class="hljs-variable">$c</span> &lt;- tcga<span class="hljs-variable">$c</span><span class="hljs-selector-attr">[,rownames(tcga$pca)]</span><br>tcga<span class="hljs-variable">$g</span> &lt;- tcga<span class="hljs-variable">$g</span><span class="hljs-selector-attr">[rownames(tcga$pca)]</span><br>tcga<span class="hljs-variable">$deg</span> &lt;- <span class="hljs-built_in">f_dds</span>(tcga<span class="hljs-variable">$c</span>, tcga<span class="hljs-variable">$g</span>, t_low=<span class="hljs-number">10</span>)<br>tcga<span class="hljs-variable">$logFC_cutoff</span> &lt;- <span class="hljs-built_in">mean</span>(<span class="hljs-built_in">abs</span>(tcga<span class="hljs-variable">$deg</span><span class="hljs-variable">$log2FoldChange</span>)) + <span class="hljs-number">2</span>*<span class="hljs-built_in">sd</span>(<span class="hljs-built_in">abs</span>(tcga<span class="hljs-variable">$deg</span><span class="hljs-variable">$log2FoldChange</span>))<br><span class="hljs-function"><span class="hljs-title">f_DEG_Volcano</span><span class="hljs-params">(tcga<span class="hljs-variable">$deg</span><span class="hljs-variable">$log2FoldChange</span>, tcga<span class="hljs-variable">$deg</span><span class="hljs-variable">$padj</span>, rownames(tcga<span class="hljs-variable">$deg</span>)</span></span>, Threshold_logFC = <span class="hljs-built_in">mean</span>(<span class="hljs-built_in">abs</span>(tcga<span class="hljs-variable">$deg</span><span class="hljs-variable">$log2FoldChange</span>)) + <span class="hljs-number">2</span>*<span class="hljs-built_in">sd</span>(<span class="hljs-built_in">abs</span>(tcga<span class="hljs-variable">$deg</span><span class="hljs-variable">$log2FoldChange</span>)), lc_p_m = <span class="hljs-number">1</span>e-<span class="hljs-number">300</span>)<br></code></pre></td></tr></table></figure>
                
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