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            <h1 id="seo-header">不同批次但未记录批次时使用DESeq2的方法</h1>
            
            
              <div class="markdown-body">
                
                <h2 id="准备数据"><a href="#准备数据" class="headerlink" title="准备数据"></a>准备数据</h2><figure class="highlight r"><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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>SummarizedExperiment<span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> load<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;PRAD_tp.rda&#x27;</span><span class="hljs-punctuation">)</span><br>counts <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>assays<span class="hljs-operator">@</span>data<span class="hljs-operator">$</span>unstranded<br>colnames<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>colData<span class="hljs-operator">$</span>patient<br>f_rm_duplicated <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>NameL<span class="hljs-punctuation">,</span> reverse<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    tmp <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>table<span class="hljs-punctuation">(</span>NameL<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>reverse<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>NameL<span class="hljs-punctuation">[</span>tmp<span class="hljs-operator">$</span>Freq <span class="hljs-operator">&gt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>NameL<span class="hljs-punctuation">[</span>tmp<span class="hljs-operator">$</span>Freq <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><br>    which<span class="hljs-punctuation">(</span>NameL <span class="hljs-operator">%in%</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>counts <span class="hljs-operator">&lt;-</span> counts<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>f_rm_duplicated<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>geneInfo <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>data<span class="hljs-operator">@</span>rowRanges<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;gene_id&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;gene_type&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;gene_name&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>tmp <span class="hljs-operator">&lt;-</span> load<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;mCRPC.rda&#x27;</span><span class="hljs-punctuation">)</span><br>geneInfo2 <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>data<span class="hljs-operator">@</span>rowRanges<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;gene_id&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;gene_type&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;gene_name&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br><span class="hljs-built_in">all</span><span class="hljs-punctuation">(</span>geneInfo2<span class="hljs-operator">$</span>gene_id <span class="hljs-operator">==</span> geneInfo<span class="hljs-operator">$</span>gene_id<span class="hljs-punctuation">)</span><br>counts2 <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>assays<span class="hljs-operator">@</span>data<span class="hljs-operator">$</span>unstranded<br>colnames<span class="hljs-punctuation">(</span>counts2<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>colData<span class="hljs-operator">$</span>bcr_patient_barcode<br>counts2 <span class="hljs-operator">&lt;-</span> counts2<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>f_rm_duplicated<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>counts2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>colnames<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;N&#x27;</span><span class="hljs-punctuation">,</span> colnames<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sep <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">)</span><br>cts_b <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>cbind<span class="hljs-punctuation">(</span>counts2<span class="hljs-punctuation">,</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>rownames<span class="hljs-punctuation">(</span>geneInfo<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>keep <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>rowSums<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span> <span class="hljs-operator">&gt;</span> ncol<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">&amp;</span> <span class="hljs-punctuation">(</span>rowSums<span class="hljs-punctuation">(</span>counts2<span class="hljs-punctuation">)</span> <span class="hljs-operator">&gt;</span> ncol<span class="hljs-punctuation">(</span>counts2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br></code></pre></td></tr></table></figure>

<h2 id="安装补充包"><a href="#安装补充包" class="headerlink" title="安装补充包"></a>安装补充包</h2><ul>
<li><a href="https://occdn.limour.top/1653.html">conda activate tcga</a></li>
<li>conda install -c bioconda bioconductor-sva -y</li>
</ul>
<h2 id="计算DEG"><a href="#计算DEG" class="headerlink" title="计算DEG"></a>计算DEG</h2><figure class="highlight r"><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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>DESeq2<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>sva<span class="hljs-punctuation">)</span><br>f_DESeq2_sva <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cts_bb<span class="hljs-punctuation">,</span> rowInfo<span class="hljs-punctuation">,</span> ControlN<span class="hljs-punctuation">,</span> TreatN<span class="hljs-punctuation">,</span> rm.NA<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    cts_b <span class="hljs-operator">&lt;-</span> cts_bb<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>ControlN<span class="hljs-punctuation">,</span> TreatN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    conditions <span class="hljs-operator">&lt;-</span> factor<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Control&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>ControlN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Treat&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>TreatN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <br>    colData_b <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> colnames<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> conditions<span class="hljs-punctuation">)</span><br>    <span class="hljs-comment">## 生物学差异的设计矩阵</span><br>    group <span class="hljs-operator">&lt;-</span> as.factor<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Ctl&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>ControlN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Trt&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>TreatN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    mod1  <span class="hljs-operator">&lt;-</span>  model.matrix<span class="hljs-punctuation">(</span><span class="hljs-operator">~</span>group<span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>mod1<span class="hljs-punctuation">)</span><br>    <span class="hljs-comment">## 无差异的设计矩阵</span><br>    mod0  <span class="hljs-operator">&lt;-</span>  cbind<span class="hljs-punctuation">(</span>mod1<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    svseq  <span class="hljs-operator">&lt;-</span>  svaseq<span class="hljs-punctuation">(</span>as.matrix<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>mod1<span class="hljs-punctuation">,</span>mod0<span class="hljs-punctuation">,</span>n.sv<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># Estimate batch with svaseq (unsupervised)</span><br>    colData_b<span class="hljs-operator">$</span>SVa <span class="hljs-operator">&lt;-</span> svseq<span class="hljs-operator">$</span>sv<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    colData_b<span class="hljs-operator">$</span>SVb <span class="hljs-operator">&lt;-</span> svseq<span class="hljs-operator">$</span>sv<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><br>    print<span class="hljs-punctuation">(</span>colData_b<span class="hljs-punctuation">)</span><br>    ddssva <span class="hljs-operator">&lt;-</span> DESeqDataSetFromMatrix<span class="hljs-punctuation">(</span>countData <span class="hljs-operator">=</span> cts_b<span class="hljs-punctuation">,</span><br>                          colData <span class="hljs-operator">=</span> colData_b<span class="hljs-punctuation">,</span><br>                          design <span class="hljs-operator">=</span> <span class="hljs-operator">~</span> SVa <span class="hljs-operator">+</span> SVb <span class="hljs-operator">+</span> conditions<span class="hljs-punctuation">)</span><br>    ddssva <span class="hljs-operator">&lt;-</span> DESeq<span class="hljs-punctuation">(</span>ddssva<span class="hljs-punctuation">)</span><br>    <br>    res <span class="hljs-operator">&lt;-</span> results<span class="hljs-punctuation">(</span>ddssva<span class="hljs-punctuation">,</span> contrast<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;conditions&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;Treat&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;Control&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    rres <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>rowInfo<span class="hljs-punctuation">,</span> data.frame<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>rm.NA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>rres <span class="hljs-operator">&lt;-</span> rres<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>rres<span class="hljs-operator">$</span>padj<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">&#125;</span><br>    rres <span class="hljs-operator">&lt;-</span> rres<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>rres<span class="hljs-operator">$</span>log2FoldChange<span class="hljs-punctuation">,</span> decreasing <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-comment"># saveRDS(rres, paste(&#x27;DEGs&#x27;, paste(TreatN, collapse = &#x27;_&#x27;), &#x27;vs.&#x27;, paste(ControlN, collapse = &#x27;_&#x27;), &#x27;DESeq2.rds&#x27;,sep = &#x27;_&#x27;))</span><br>    rres<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><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 R">Ct1 <span class="hljs-operator">&lt;-</span> colnames<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><br>Tt1 <span class="hljs-operator">&lt;-</span> colnames<span class="hljs-punctuation">(</span>counts2<span class="hljs-punctuation">)</span><br>r1 <span class="hljs-operator">&lt;-</span> f_DESeq2_sva<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> geneInfo<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> Ct1<span class="hljs-punctuation">,</span> Tt1<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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