ryan
/
resume
镜像自地址 https://github.com/DarwinAwardWinner/resume.git


			
				
					
						
						
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<h2></h2>

<div class="highlight"><pre><span></span><span class="c1">## Load packages</span>
<span class="kn">library</span><span class="p">(</span>openxlsx<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>affy<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>frma<span class="p">)</span>

<span class="c1">## Load the fRMA data package and then load the data</span>
<span class="kn">library</span><span class="p">(</span>DSalomon.PAX.hthgu133pluspmfrmavecs<span class="p">)</span>
data<span class="p">(</span>DSalomon.PAX.hthgu133pluspmfrmavecs<span class="p">)</span>

<span class="c1">## Get the sample table and list of CEL files</span>
cel.dir <span class="o">&lt;-</span> <span class="s">&quot;Training Data/01 - CTOT08 ABECASSIS PAX Samples&quot;</span>
<span class="c1">## Read the first xlsx file in the directory, which is a spreadsheet</span>
<span class="c1">## containing all of the CEL file names</span>
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>
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>

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

<span class="c1">## Apply fRMA</span>
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>

<span class="c1">## Extract expression matrix</span>
expr <span class="o">&lt;-</span> exprs<span class="p">(</span>eset<span class="p">)</span>

<span class="c1">## Extract sample table</span>
sample.table <span class="o">&lt;-</span> pData<span class="p">(</span>eset<span class="p">)</span>
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