ryan
/
resume
mirror de https://github.com/DarwinAwardWinner/resume.git


			
				
					
						
						
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<h2></h2>

<div class="highlight"><pre><span></span><span class="c1">#!/usr/bin/env Rscript</span>

<span class="kn">library</span><span class="p">(</span>xlsx<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>frma<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>frmaTools<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>stringr<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>magrittr<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>plyr<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>preprocessCore<span class="p">)</span>

training.data.dir <span class="o">&lt;-</span> <span class="s">&quot;Training Data&quot;</span>
datasets <span class="o">&lt;-</span> <span class="kt">data.frame</span><span class="p">(</span>Dataset<span class="o">=</span><span class="kp">list.files</span><span class="p">(</span>training.data.dir<span class="p">))</span>
<span class="kp">rownames</span><span class="p">(</span>datasets<span class="p">)</span> <span class="o">&lt;-</span> datasets<span class="o">$</span>Dataset
datasets<span class="o">$</span>Tissue <span class="o">&lt;-</span> <span class="kp">factor</span><span class="p">(</span>str_extract<span class="p">(</span>datasets<span class="o">$</span>Dataset<span class="p">,</span> <span class="s">&quot;\\b(PAX|BX)\\b&quot;</span><span class="p">))</span>

tsmsg <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span><span class="kc">...</span><span class="p">)</span> <span class="p">{</span>
  <span class="kp">message</span><span class="p">(</span><span class="kp">date</span><span class="p">(),</span> <span class="s">&quot;: &quot;</span><span class="p">,</span> <span class="kc">...</span><span class="p">)</span>
<span class="p">}</span>

parse.date.from.filename <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>fname<span class="p">)</span> <span class="p">{</span>
    res1 <span class="o">&lt;-</span> str_match<span class="p">(</span>fname<span class="p">,</span> <span class="s">&quot;^(\\d\\d)(\\d\\d)(\\d\\d)&quot;</span><span class="p">)[,</span><span class="kt">c</span><span class="p">(</span><span class="m">4</span><span class="p">,</span><span class="m">2</span><span class="p">,</span><span class="m">3</span><span class="p">)]</span>
    res2 <span class="o">&lt;-</span> str_match<span class="p">(</span>fname<span class="p">,</span> <span class="s">&quot;^20(\\d\\d)_(\\d\\d)_(\\d\\d)&quot;</span><span class="p">)[,</span><span class="m">-1</span><span class="p">]</span>
    res1<span class="p">[</span><span class="kp">is.na</span><span class="p">(</span>res1<span class="p">)]</span> <span class="o">&lt;-</span> res2<span class="p">[</span><span class="kp">is.na</span><span class="p">(</span>res1<span class="p">)]</span>
    <span class="kp">colnames</span><span class="p">(</span>res1<span class="p">)</span> <span class="o">&lt;-</span> <span class="kt">c</span><span class="p">(</span><span class="s">&quot;year&quot;</span><span class="p">,</span> <span class="s">&quot;month&quot;</span><span class="p">,</span> <span class="s">&quot;day&quot;</span><span class="p">)</span>
    res1<span class="p">[,</span><span class="s">&quot;year&quot;</span><span class="p">]</span> <span class="o">%&lt;&gt;%</span> str_c<span class="p">(</span><span class="s">&quot;20&quot;</span><span class="p">,</span> <span class="m">.</span><span class="p">)</span>
    <span class="kp">as.Date</span><span class="p">(</span><span class="kp">do.call</span><span class="p">(</span><span class="kp">ISOdate</span><span class="p">,</span> <span class="kt">data.frame</span><span class="p">(</span>res1<span class="p">)))</span>
<span class="p">}</span>

sample.tables <span class="o">&lt;-</span> ddply<span class="p">(</span>datasets<span class="p">,</span> <span class="m">.</span><span class="p">(</span>Dataset<span class="p">),</span> <span class="kr">function</span><span class="p">(</span>df<span class="p">)</span> <span class="p">{</span>
    df <span class="o">&lt;-</span> df<span class="p">[</span><span class="m">1</span><span class="p">,]</span>
    <span class="kp">rownames</span><span class="p">(</span>df<span class="p">)</span> <span class="o">&lt;-</span> <span class="kc">NULL</span>
    dset.dir <span class="o">&lt;-</span> <span class="kp">file.path</span><span class="p">(</span>training.data.dir<span class="p">,</span> df<span class="o">$</span>Dataset<span class="p">)</span>
    x <span class="o">&lt;-</span> read.xlsx<span class="p">(</span><span class="kp">list.files</span><span class="p">(</span>dset.dir<span class="p">,</span> pattern<span class="o">=</span>glob2rx<span class="p">(</span><span class="s">&quot;*.xlsx&quot;</span><span class="p">),</span> full.names<span class="o">=</span><span class="kc">TRUE</span><span class="p">)[</span><span class="m">1</span><span class="p">],</span> <span class="m">1</span><span class="p">)</span> <span class="o">%&gt;%</span>
        setNames<span class="p">(</span><span class="kt">c</span><span class="p">(</span><span class="s">&quot;Filename&quot;</span><span class="p">,</span> <span class="s">&quot;Phenotype&quot;</span><span class="p">,</span> <span class="s">&quot;ScanDate&quot;</span><span class="p">))</span>
    x<span class="o">$</span>Filename <span class="o">&lt;-</span> <span class="kp">as.character</span><span class="p">(</span>x<span class="o">$</span>Filename<span class="p">)</span>
    missing.CEL <span class="o">&lt;-</span> <span class="o">!</span>str_detect<span class="p">(</span>x<span class="o">$</span>Filename<span class="p">,</span> <span class="s">&quot;\\.CEL$&quot;</span><span class="p">)</span>
    x<span class="o">$</span>Filename<span class="p">[</span>missing.CEL<span class="p">]</span> <span class="o">&lt;-</span> str_c<span class="p">(</span>x<span class="o">$</span>Filename<span class="p">[</span>missing.CEL<span class="p">],</span> <span class="s">&quot;.CEL&quot;</span><span class="p">)</span>
    <span class="kp">stopifnot</span><span class="p">(</span><span class="kp">all</span><span class="p">(</span>str_detect<span class="p">(</span>x<span class="o">$</span>Filename<span class="p">,</span> <span class="s">&quot;\\.CEL$&quot;</span><span class="p">)))</span>
    parsed.date <span class="o">&lt;-</span> parse.date.from.filename<span class="p">(</span>x<span class="o">$</span>Filename<span class="p">)</span>
    x<span class="o">$</span>ScanDate<span class="p">[</span><span class="o">!</span><span class="kp">is.na</span><span class="p">(</span>parsed.date<span class="p">)]</span> <span class="o">&lt;-</span> parsed.date<span class="p">[</span><span class="o">!</span><span class="kp">is.na</span><span class="p">(</span>parsed.date<span class="p">)]</span>
    x <span class="o">%&gt;%</span> <span class="kp">cbind</span><span class="p">(</span>df<span class="p">)</span> <span class="o">%&gt;%</span>
        <span class="kp">transform</span><span class="p">(</span>Filename<span class="o">=</span><span class="kp">file.path</span><span class="p">(</span>dset.dir<span class="p">,</span> Filename<span class="p">),</span>
                  Batch<span class="o">=</span><span class="kp">droplevels</span><span class="p">(</span>Tissue<span class="o">:</span>Dataset<span class="o">:</span><span class="kp">factor</span><span class="p">(</span>ScanDate<span class="p">)</span><span class="o">:</span>Phenotype<span class="p">))</span> <span class="o">%&gt;%</span>
                      <span class="kp">subset</span><span class="p">(</span><span class="o">!</span> Filename <span class="o">%in%</span> blacklist<span class="p">)</span>
<span class="p">})</span> <span class="o">%&gt;%</span> <span class="kp">split</span><span class="p">(</span><span class="m">.</span><span class="o">$</span>Tissue<span class="p">)</span> <span class="o">%&gt;%</span> <span class="kp">lapply</span><span class="p">(</span><span class="kp">droplevels</span><span class="p">)</span>

annotation <span class="o">&lt;-</span> cleancdfname<span class="p">(</span>affyio<span class="o">:::</span>read.celfile.header<span class="p">(</span>sample.tables<span class="p">[[</span><span class="m">1</span><span class="p">]]</span><span class="o">$</span>Filename<span class="p">[</span><span class="m">1</span><span class="p">])</span><span class="o">$</span>cdfName<span class="p">,</span> <span class="kc">FALSE</span><span class="p">)</span>

esets <span class="o">&lt;-</span> <span class="kt">list</span><span class="p">()</span>

<span class="kr">for</span> <span class="p">(</span>i <span class="kr">in</span> <span class="kp">names</span><span class="p">(</span>sample.tables<span class="p">))</span> <span class="p">{</span>
    pkgname <span class="o">&lt;-</span> <span class="kp">sprintf</span><span class="p">(</span><span class="s">&quot;DSalomon.%s.%sfrmavecs&quot;</span><span class="p">,</span> i<span class="p">,</span> annotation<span class="p">)</span>
    <span class="kp">message</span><span class="p">(</span><span class="s">&quot;Loading &quot;</span><span class="p">,</span> pkgname<span class="p">)</span>
    <span class="kn">require</span><span class="p">(</span>pkgname<span class="p">,</span> character.only<span class="o">=</span><span class="kc">TRUE</span><span class="p">,</span> quietly<span class="o">=</span><span class="kc">TRUE</span><span class="p">)</span>
    data<span class="p">(</span><span class="kt">list</span> <span class="o">=</span> pkgname<span class="p">)</span>

    <span class="kp">message</span><span class="p">(</span><span class="s">&quot;Loading raw data for &quot;</span><span class="p">,</span> i<span class="p">)</span>
    stab <span class="o">&lt;-</span> sample.tables<span class="p">[[</span>i<span class="p">]]</span>
    affy <span class="o">&lt;-</span> ReadAffy<span class="p">(</span>filenames<span class="o">=</span>stab<span class="o">$</span>Filename<span class="p">,</span> phenoData<span class="o">=</span>stab<span class="p">)</span>

    <span class="kp">message</span><span class="p">(</span><span class="s">&quot;Running fRMA for &quot;</span><span class="p">,</span> i<span class="p">)</span>
    esets<span class="p">[[</span>i<span class="p">]]</span> <span class="o">&lt;-</span> frma<span class="p">(</span>affy<span class="p">,</span> input.vecs<span class="o">=</span><span class="kp">get</span><span class="p">(</span>pkgname<span class="p">),</span> verbose<span class="o">=</span><span class="kc">TRUE</span><span class="p">)</span>
    <span class="kp">rm</span><span class="p">(</span>affy<span class="p">)</span>
    <span class="kp">gc</span><span class="p">()</span>
<span class="p">}</span>
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