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            <h1 id="seo-header">TCGAbiolinks下载甲基化数据</h1>
            
            
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                <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 target="_blank" rel="noopener" href="https://occdn.limour.top/1655.html">conda activate tcga</a></li>
<li># conda install -c bioconda bioconductor-sesamedata -y</li>
<li>conda install -c conda-forge r-magick -y</li>
<li>BiocManager::install(“sesameData”)</li>
<li>BiocManager::install(“sesame”)</li>
<li>BiocManager::install(“doParallel”)</li>
<li>BiocManager::install(“ComplexHeatmap”)</li>
<li>BiocManager::install(“matlab”)</li>
<li>conda install -c bioconda bioconductor-motifstack -y</li>
<li># conda install -c bioconda bioconductor-bsgenome.hsapiens.ucsc.hg38 -y</li>
<li>BiocManager::install(“BSgenome.Hsapiens.UCSC.hg38”)</li>
<li>BiocManager::install(“BSgenome.Hsapiens.UCSC.hg19”)</li>
<li># conda install -c bioconda bioconductor-genomicranges -y</li>
<li>conda install -c bioconda bioconductor-rgadem -y</li>
</ul>
<h2 id="下载数据"><a href="#下载数据" class="headerlink" title="下载数据"></a>下载数据</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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>TCGAbiolinks<span class="hljs-punctuation">)</span><br>query_met.hg38 <span class="hljs-operator">&lt;-</span> GDCquery<span class="hljs-punctuation">(</span><br>    project<span class="hljs-operator">=</span> <span class="hljs-string">&quot;TCGA-PRAD&quot;</span><span class="hljs-punctuation">,</span> <br>    data.category <span class="hljs-operator">=</span> <span class="hljs-string">&quot;DNA Methylation&quot;</span><span class="hljs-punctuation">,</span> <br>    data.type <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Methylation Beta Value&quot;</span><span class="hljs-punctuation">,</span><br>    platform <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Illumina Human Methylation 450&quot;</span><br><span class="hljs-punctuation">)</span><br>GDCdownload<span class="hljs-punctuation">(</span>query_met.hg38<span class="hljs-punctuation">)</span><br>data.hg38 <span class="hljs-operator">&lt;-</span> GDCprepare<span class="hljs-punctuation">(</span>query_met.hg38<span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;prad.meth.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="清洗数据"><a href="#清洗数据" class="headerlink" title="清洗数据"></a>清洗数据</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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>SummarizedExperiment<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># 删除包含 NA 值的探针</span><br>data.hg38 <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">,</span>subset <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span>rowSums<span class="hljs-punctuation">(</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>assay<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># 去除重复样本</span><br>data.hg38 <span class="hljs-operator">&lt;-</span> data.hg38<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> substr<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-number">14</span><span class="hljs-punctuation">,</span> <span class="hljs-number">16</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-string">&quot;01A&quot;</span><span class="hljs-punctuation">]</span><br>group <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../idea_2/fig3.2/fig5/tcga.predict.rds&#x27;</span><span class="hljs-punctuation">)</span><br>gRow <span class="hljs-operator">&lt;-</span> intersect<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-operator">$</span>patient<span class="hljs-punctuation">,</span> rownames<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>group <span class="hljs-operator">&lt;-</span> group<span class="hljs-punctuation">[</span>gRow<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>data.hg38 <span class="hljs-operator">&lt;-</span> data.hg38<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> substr<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%in%</span> gRow<span class="hljs-punctuation">]</span><br>data.hg38<span class="hljs-operator">$</span>group <span class="hljs-operator">&lt;-</span> group<span class="hljs-punctuation">[</span>substr<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;group&#x27;</span><span class="hljs-punctuation">]</span><br></code></pre></td></tr></table></figure>

<h2 id="计算整体差异"><a href="#计算整体差异" class="headerlink" title="计算整体差异"></a>计算整体差异</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></pre></td><td class="code"><pre><code class="hljs R">TCGAvisualize_meanMethylation<span class="hljs-punctuation">(</span><br>  data.hg38<span class="hljs-punctuation">,</span><br>  groupCol <span class="hljs-operator">=</span> <span class="hljs-string">&quot;group&quot;</span><span class="hljs-punctuation">,</span><br>  group.legend  <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Groups&quot;</span><span class="hljs-punctuation">,</span><br>  filename <span class="hljs-operator">=</span> <span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span><br>  print.pvalue <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><br><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="识别差异甲基化-CpG-位点"><a href="#识别差异甲基化-CpG-位点" class="headerlink" title="识别差异甲基化 CpG 位点"></a><strong>识别差异甲基化</strong> CpG <strong>位点</strong></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">res <span class="hljs-operator">&lt;-</span> TCGAanalyze_DMC<span class="hljs-punctuation">(</span><br>  data.hg38<span class="hljs-punctuation">,</span><br>  <span class="hljs-comment"># colData 函数获取的矩阵中分组列名</span><br>  groupCol <span class="hljs-operator">=</span> <span class="hljs-string">&quot;group&quot;</span><span class="hljs-punctuation">,</span><br>  group1 <span class="hljs-operator">=</span> <span class="hljs-string">&quot;High Risk&quot;</span><span class="hljs-punctuation">,</span><br>  group2 <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Low Risk&quot;</span><span class="hljs-punctuation">,</span><br>  p.cut <span class="hljs-operator">=</span> <span class="hljs-number">0.05</span><span class="hljs-punctuation">,</span><br>  diffmean.cut <span class="hljs-operator">=</span> <span class="hljs-number">0.15</span><span class="hljs-punctuation">,</span><br>  save <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>  legend <span class="hljs-operator">=</span> <span class="hljs-string">&quot;State&quot;</span><span class="hljs-punctuation">,</span><br>  plot.filename <span class="hljs-operator">=</span> <span class="hljs-string">&quot;./PRAD_metvolcano.png&quot;</span><span class="hljs-punctuation">,</span><br>  cores <span class="hljs-operator">=</span>  <span class="hljs-number">8</span><br><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="绘制热图"><a href="#绘制热图" class="headerlink" title="绘制热图"></a>绘制热图</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><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">sig_met <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> status <span class="hljs-operator">!=</span> <span class="hljs-string">&quot;Not Significant&quot;</span><span class="hljs-punctuation">)</span><br>res_data <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">,</span> subset <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">)</span> <span class="hljs-operator">%in%</span> rownames<span class="hljs-punctuation">(</span>sig_met<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>circlize<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ComplexHeatmap<span class="hljs-punctuation">)</span><br>group <span class="hljs-operator">&lt;-</span> group<span class="hljs-punctuation">[</span>substr<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span><br><span class="hljs-comment">#定义注释信息</span><br>ha <span class="hljs-operator">&lt;-</span> HeatmapAnnotation<span class="hljs-punctuation">(</span>`Risk group` <span class="hljs-operator">=</span> group<span class="hljs-operator">$</span>group<span class="hljs-punctuation">,</span><br>                        `Risk Score` <span class="hljs-operator">=</span> group<span class="hljs-operator">$</span>Risk_Score<span class="hljs-punctuation">,</span><br>                        col <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><br>                            `Risk group` <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Low Risk&quot;</span> <span class="hljs-operator">=</span> <span class="hljs-string">&quot;#99CCFFAA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;High Risk&#x27;</span> <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;#FF6666AA&#x27;</span><span class="hljs-punctuation">)</span><br>                        <span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br><span class="hljs-comment">#                         annotation_name_gp = gpar(fontsize = 14),</span><br>                        show_annotation_name <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>heatmap  <span class="hljs-operator">&lt;-</span> Heatmap<span class="hljs-punctuation">(</span><br>  assay<span class="hljs-punctuation">(</span>res_data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>  name <span class="hljs-operator">=</span> <span class="hljs-string">&quot;DNA methylation&quot;</span><span class="hljs-punctuation">,</span><br>  col <span class="hljs-operator">=</span> matlab<span class="hljs-operator">::</span>jet.colors<span class="hljs-punctuation">(</span><span class="hljs-number">200</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>  show_row_names <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>  cluster_rows <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span><br>  cluster_columns <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>  show_column_names <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>  bottom_annotation <span class="hljs-operator">=</span> ha<span class="hljs-punctuation">,</span><br>  column_title <span class="hljs-operator">=</span> <span class="hljs-string">&quot;DNA Methylation&quot;</span><span class="hljs-punctuation">,</span><br>  column_order <span class="hljs-operator">=</span> order<span class="hljs-punctuation">(</span>group<span class="hljs-operator">$</span>Risk_Score<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">)</span><br>pdf<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;./prad_meth_heatmap.pdf&quot;</span><span class="hljs-punctuation">,</span>width <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">4</span><span class="hljs-punctuation">)</span>;<span class="hljs-punctuation">&#123;</span><br>    draw<span class="hljs-punctuation">(</span>heatmap<span class="hljs-punctuation">,</span> annotation_legend_side <span class="hljs-operator">=</span>  <span class="hljs-string">&quot;bottom&quot;</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span>;dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="模体分析（需要hg19）"><a href="#模体分析（需要hg19）" class="headerlink" title="模体分析（需要hg19）"></a><strong>模体分析</strong>（需要hg19）</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></pre></td><td class="code"><pre><code class="hljs R">query_met.hg19 <span class="hljs-operator">&lt;-</span> GDCquery<span class="hljs-punctuation">(</span><br>    project<span class="hljs-operator">=</span> <span class="hljs-string">&quot;TCGA-PRAD&quot;</span><span class="hljs-punctuation">,</span> <br>    data.category <span class="hljs-operator">=</span> <span class="hljs-string">&quot;DNA methylation&quot;</span><span class="hljs-punctuation">,</span><br>    platform <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Illumina Human Methylation 450&quot;</span><span class="hljs-punctuation">,</span><br>    legacy <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span> <span class="hljs-comment"># hg19</span><br><span class="hljs-punctuation">)</span><br>GDCdownload<span class="hljs-punctuation">(</span>query_met.hg19<span class="hljs-punctuation">)</span><br>data.hg19 <span class="hljs-operator">&lt;-</span> GDCprepare<span class="hljs-punctuation">(</span>query_met.hg19<span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>data.hg38<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;prad.meth.hg19.rds&#x27;</span><span class="hljs-punctuation">)</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><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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>rGADEM<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>GenomicRanges<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>BSgenome.Hsapiens.UCSC.hg19<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>motifStack<span class="hljs-punctuation">)</span><br>probes <span class="hljs-operator">&lt;-</span> rowRanges<span class="hljs-punctuation">(</span>res_data<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># 获取差异的探针并设置 200bp 大小的窗口</span><br>sequence <span class="hljs-operator">&lt;-</span> GRanges<span class="hljs-punctuation">(</span><br>  seqnames <span class="hljs-operator">=</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>seqnames<span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>  ranges <span class="hljs-operator">=</span> IRanges<span class="hljs-punctuation">(</span>start <span class="hljs-operator">=</span> start<span class="hljs-punctuation">(</span>ranges<span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">-</span> <span class="hljs-number">100</span><span class="hljs-punctuation">,</span><br>          end <span class="hljs-operator">=</span> start<span class="hljs-punctuation">(</span>ranges<span class="hljs-punctuation">(</span>probes<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <span class="hljs-number">100</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>  strand <span class="hljs-operator">=</span> <span class="hljs-string">&quot;*&quot;</span><br><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># 识别模体</span><br>gadem <span class="hljs-operator">&lt;-</span> GADEM<span class="hljs-punctuation">(</span>sequence<span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span> genome <span class="hljs-operator">=</span> Hsapiens<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<p>因为hg19的数据还在下载，更多内容见<a target="_blank" rel="noopener" href="https://www.bioconductor.org/packages/release/workflows/vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.html">官方教程</a></p>

                
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