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            <h1 id="seo-header">【迁移】使用FindTransferAnchors对样本进行预注释</h1>
            
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                    Last updated on March 19, 2024 pm
                  
                
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                <h2 id="处理参考样本">处理参考样本</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></pre></td><td class="code"><pre><code class="hljs R">ref_sce <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;~/upload/zl_liu/data/pca.rds&#x27;</span><span class="hljs-punctuation">)</span><br>ref_sce <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">,</span> group <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;CRPC&#x27;</span><span class="hljs-punctuation">)</span><br>table<span class="hljs-punctuation">(</span>ref_sce<span class="hljs-operator">@</span>meta.data<span class="hljs-operator">$</span>cell_type_fig3<span class="hljs-punctuation">)</span><br>g2m_genes <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>CaseMatch<span class="hljs-punctuation">(</span>search<span class="hljs-operator">=</span>Seurat<span class="hljs-operator">::</span>cc.genes<span class="hljs-operator">$</span>g2m.genes<span class="hljs-punctuation">,</span> <br>                               match<span class="hljs-operator">=</span>rownames<span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>s_genes <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>CaseMatch<span class="hljs-punctuation">(</span>search<span class="hljs-operator">=</span>Seurat<span class="hljs-operator">::</span>cc.genes<span class="hljs-operator">$</span>s.genes<span class="hljs-punctuation">,</span> <br>                             match<span class="hljs-operator">=</span>rownames<span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>ref_sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>CellCycleScoring<span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">,</span> g2m.features<span class="hljs-operator">=</span>g2m_genes<span class="hljs-punctuation">,</span> s.features<span class="hljs-operator">=</span>s_genes<span class="hljs-punctuation">)</span><br>ref_sce<span class="hljs-operator">$</span>CC.Difference <span class="hljs-operator">&lt;-</span> ref_sce<span class="hljs-operator">$</span>S.Score <span class="hljs-operator">-</span> ref_sce<span class="hljs-operator">$</span>G2M.Score <br>ref_sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>PercentageFeatureSet<span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^MT-&quot;</span><span class="hljs-punctuation">)</span><br>ref_sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.ERCC&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>PercentageFeatureSet<span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^ERCC-&quot;</span><span class="hljs-punctuation">)</span><br>ref_sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.rp&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>PercentageFeatureSet<span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^RP[SL]&quot;</span><span class="hljs-punctuation">)</span><br>ref_sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>SplitObject<span class="hljs-punctuation">(</span>object <span class="hljs-operator">=</span> ref_sce<span class="hljs-punctuation">,</span> split.by <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;orig.ident&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h3 id="integration">integration</h3>
<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></pre></td><td class="code"><pre><code class="hljs R">ref_sce <span class="hljs-operator">&lt;-</span> lapply<span class="hljs-punctuation">(</span>X <span class="hljs-operator">=</span> ref_sce<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">&#123;</span><br>    x <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>SCTransform<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> vst.flavor <span class="hljs-operator">=</span> <span class="hljs-string">&quot;v2&quot;</span><span class="hljs-punctuation">,</span><br>                           vars.to.regress <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;CC.Difference&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;percent.rp&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                           verbose <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>features <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>SelectIntegrationFeatures<span class="hljs-punctuation">(</span>object.list <span class="hljs-operator">=</span> ref_sce<span class="hljs-punctuation">,</span> <br>                                              assay <span class="hljs-operator">=</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;SCT&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>ref_sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>PrepSCTIntegration<span class="hljs-punctuation">(</span>object.list <span class="hljs-operator">=</span> ref_sce<span class="hljs-punctuation">,</span> <br>                                      anchor.features <span class="hljs-operator">=</span> features<span class="hljs-punctuation">,</span> <br>                                      assay <span class="hljs-operator">=</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;SCT&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>anchors <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>FindIntegrationAnchors<span class="hljs-punctuation">(</span>object.list <span class="hljs-operator">=</span> ref_sce<span class="hljs-punctuation">,</span> <br>                                          normalization.method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;SCT&quot;</span><span class="hljs-punctuation">,</span><br>                                          anchor.features <span class="hljs-operator">=</span> features<span class="hljs-punctuation">,</span> <br>                                          assay <span class="hljs-operator">=</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;SCT&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>ref_sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>combined <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>IntegrateData<span class="hljs-punctuation">(</span>anchorset <span class="hljs-operator">=</span> anchors<span class="hljs-punctuation">,</span><br>                                 normalization.method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;SCT&quot;</span><span class="hljs-punctuation">)</span><br>combined <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>RunPCA<span class="hljs-punctuation">(</span>combined<span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>combined <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>RunUMAP<span class="hljs-punctuation">(</span>combined<span class="hljs-punctuation">,</span> <br>                            reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;pca&quot;</span><span class="hljs-punctuation">,</span> dims <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">30</span><span class="hljs-punctuation">,</span><br>                            verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>Seurat<span class="hljs-operator">::</span>DimPlot<span class="hljs-punctuation">(</span>combined<span class="hljs-punctuation">,</span> reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;umap&quot;</span><span class="hljs-punctuation">,</span> <br>                group.by <span class="hljs-operator">=</span> <span class="hljs-string">&quot;cell_type_fig3&quot;</span><span class="hljs-punctuation">,</span><br>                repel <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> label <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h2 id="处理预处理完的样本">处理预处理完的样本</h2>
<p><a href="/shi-yong-SCTransform-biao-zhun-hua">样本来自此</a></p>
<h3 id="打个补丁">打个补丁</h3>
<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></pre></td><td class="code"><pre><code class="hljs R">sce <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;SRX6887740.rds&#x27;</span><span class="hljs-punctuation">)</span><br>Seurat<span class="hljs-operator">::</span>DefaultAssay<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;RNA&#x27;</span><br>sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.rp&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>PercentageFeatureSet<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^RP[SL]&quot;</span><span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>SCTransform<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> vst.flavor <span class="hljs-operator">=</span> <span class="hljs-string">&quot;v2&quot;</span><span class="hljs-punctuation">,</span><br>                       vars.to.regress <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;CC.Difference&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;percent.rp&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                       verbose <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h3 id="FindTransferAnchors">FindTransferAnchors</h3>
<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></pre></td><td class="code"><pre><code class="hljs R">anchors <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>FindTransferAnchors<span class="hljs-punctuation">(</span>reference <span class="hljs-operator">=</span> combined<span class="hljs-punctuation">,</span> query <span class="hljs-operator">=</span> sce<span class="hljs-punctuation">,</span><br>                                      normalization.method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;SCT&quot;</span><span class="hljs-punctuation">,</span><br>                                      reference.assay <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;integrated&#x27;</span><span class="hljs-punctuation">,</span><br>                                      query.assay <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;SCT&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h3 id="TransferData">TransferData</h3>
<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">predictions <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>TransferData<span class="hljs-punctuation">(</span>anchorset <span class="hljs-operator">=</span> anchors<span class="hljs-punctuation">,</span> <br>                            refdata <span class="hljs-operator">=</span> combined<span class="hljs-operator">$</span>cell_type_fig3<span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> AddMetaData<span class="hljs-punctuation">(</span>object <span class="hljs-operator">=</span> sce<span class="hljs-punctuation">,</span> metadata <span class="hljs-operator">=</span> predictions<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h3 id="可视化">可视化</h3>
<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></pre></td><td class="code"><pre><code class="hljs R">sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>RunPCA<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>RunUMAP<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;pca&quot;</span><span class="hljs-punctuation">,</span> <br>                       dims <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">30</span><span class="hljs-punctuation">,</span> <br>                       verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>Seurat<span class="hljs-operator">::</span>DimPlot<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;umap&quot;</span><span class="hljs-punctuation">,</span> <br>                group.by <span class="hljs-operator">=</span> <span class="hljs-string">&quot;predicted.id&quot;</span><span class="hljs-punctuation">,</span><br>                repel <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> label <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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