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run-frma-example.R.html

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  85. <h2></h2>
    86. 

  86. 

  87. <div class="highlight"><pre><span></span><span class="c1">## Load packages</span>
    88. 

  88. <span class="kn">library</span><span class="p">(</span>openxlsx<span class="p">)</span>
    89. 

  89. <span class="kn">library</span><span class="p">(</span>affy<span class="p">)</span>
    90. 

  90. <span class="kn">library</span><span class="p">(</span>frma<span class="p">)</span>
    91. 

  91. 

  92. <span class="c1">## Load the fRMA data package and then load the data</span>
    93. 

  93. <span class="kn">library</span><span class="p">(</span>DSalomon.PAX.hthgu133pluspmfrmavecs<span class="p">)</span>
    94. 

  94. data<span class="p">(</span>DSalomon.PAX.hthgu133pluspmfrmavecs<span class="p">)</span>
    95. 

  95. 

  96. <span class="c1">## Get the sample table and list of CEL files</span>
    97. 

  97. cel.dir <span class="o">&lt;-</span> <span class="s">&quot;Training Data/01 - CTOT08 ABECASSIS PAX Samples&quot;</span>
    98. 

  98. <span class="c1">## Read the first xlsx file in the directory, which is a spreadsheet</span>
    99. 

  99. <span class="c1">## containing all of the CEL file names</span>
    100. 

  100. sample.table <span class="o">&lt;-</span> read.xlsx<span class="p">(</span><span class="kp">list.files</span><span class="p">(</span>cel.dir<span class="p">,</span> pattern<span class="o">=</span>glob2rx<span class="p">(</span><span class="s">&quot;*.xlsx&quot;</span><span class="p">),</span> full.names<span class="o">=</span><span class="kc">TRUE</span><span class="p">)[</span><span class="m">1</span><span class="p">])</span>
    101. 

  101. cel.files <span class="o">&lt;-</span> <span class="kp">file.path</span><span class="p">(</span>cel.dir<span class="p">,</span> sample.table<span class="o">$</span>Filename<span class="p">)</span>
    102. 

  102. 

  103. <span class="c1">## Read the data from the CEL files</span>
    104. 

  104. affy <span class="o">&lt;-</span> ReadAffy<span class="p">(</span>filenames<span class="o">=</span>cel.files<span class="p">,</span> phenoData<span class="o">=</span>sample.table<span class="p">)</span>
    105. 

  105. 

  106. <span class="c1">## Apply fRMA</span>
    107. 

  107. eset <span class="o">&lt;-</span> frma<span class="p">(</span>affy<span class="p">,</span> input.vecs<span class="o">=</span>DSalomon.PAX.hthgu133pluspmfrmavecs<span class="p">)</span>
    108. 

  108. 

  109. <span class="c1">## Extract expression matrix</span>
    110. 

  110. expr <span class="o">&lt;-</span> exprs<span class="p">(</span>eset<span class="p">)</span>
    111. 

  111. 

  112. <span class="c1">## Extract sample table</span>
    113. 

  113. sample.table <span class="o">&lt;-</span> pData<span class="p">(</span>eset<span class="p">)</span>
    114. 

  114. </pre></div>
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