ryan
/
resume
kopia lustrzana https://github.com/DarwinAwardWinner/resume.git


			
				
					
						
						
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<h2></h2>

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

<span class="kn">source</span><span class="p">(</span><span class="s">&quot;common.R&quot;</span><span class="p">)</span>

<span class="kn">library</span><span class="p">(</span>rtracklayer<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>DiffBind<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>doMC<span class="p">)</span>
registerDoMC<span class="p">()</span>
<span class="kp">options</span><span class="p">(</span>cores<span class="o">=</span>multicore<span class="o">:::</span>detectCores<span class="p">())</span>
<span class="kn">library</span><span class="p">(</span>snow<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>RColorBrewer<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>xlsx<span class="p">)</span>
<span class="kn">library</span><span class="p">(</span>edgeR<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>

tsmsgf <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>
  tsmsg<span class="p">(</span><span class="kp">sprintf</span><span class="p">(</span><span class="kc">...</span><span class="p">))</span>
<span class="p">}</span>

<span class="c1">## Additional args are passed to every call of addDataFrame</span>
write.xlsx.multisheet <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>data.frames<span class="p">,</span> <span class="kp">file</span><span class="p">,</span> sheetNames<span class="o">=</span><span class="kp">names</span><span class="p">(</span>data.frames<span class="p">),</span> <span class="kc">...</span><span class="p">)</span> <span class="p">{</span>
  <span class="kr">if</span> <span class="p">(</span><span class="kp">is.null</span><span class="p">(</span>sheetNames<span class="p">))</span> <span class="p">{</span>
    sheetNames <span class="o">&lt;-</span> str_c<span class="p">(</span><span class="s">&quot;Sheet&quot;</span><span class="p">,</span> <span class="kp">seq_along</span><span class="p">(</span>data.frames<span class="p">))</span>
  <span class="p">}</span>
  <span class="c1">## Ensure correct number of sheetNames</span>
  <span class="kp">stopifnot</span><span class="p">(</span><span class="kp">length</span><span class="p">(</span>sheetNames<span class="p">)</span> <span class="o">==</span> <span class="kp">length</span><span class="p">(</span>data.frames<span class="p">))</span>
  <span class="c1">## Fill in missing names if needed</span>
  sheetNames<span class="p">[</span><span class="kp">is.na</span><span class="p">(</span>sheetNames<span class="p">)]</span> <span class="o">&lt;-</span> str_c<span class="p">(</span><span class="s">&quot;Sheet&quot;</span><span class="p">,</span> <span class="kp">seq_along</span><span class="p">(</span>data.frames<span class="p">))[</span><span class="kp">is.na</span><span class="p">(</span>sheetNames<span class="p">)]</span>
  wb <span class="o">&lt;-</span> createWorkbook<span class="p">()</span>
  sheets <span class="o">&lt;-</span> llply<span class="p">(</span>sheetNames<span class="p">,</span> <span class="kr">function</span><span class="p">(</span>x<span class="p">)</span> createSheet<span class="p">(</span>wb<span class="p">,</span> sheetName<span class="o">=</span>x<span class="p">))</span>
  mlply<span class="p">(</span><span class="kp">cbind</span><span class="p">(</span>sheet<span class="o">=</span>sheets<span class="p">,</span> x<span class="o">=</span>data.frames<span class="p">),</span> <span class="m">.</span>fun<span class="o">=</span>addDataFrame<span class="p">,</span> <span class="m">.</span>parallel<span class="o">=</span><span class="kc">FALSE</span><span class="p">,</span> <span class="kc">...</span><span class="p">)</span>
  saveWorkbook<span class="p">(</span>wb<span class="p">,</span> <span class="kp">file</span><span class="p">)</span>
<span class="p">}</span>

renice.self <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>niceness<span class="o">=</span><span class="m">19</span><span class="p">)</span>  <span class="p">{</span>
  <span class="kp">system2</span><span class="p">(</span><span class="s">&quot;renice&quot;</span><span class="p">,</span> args<span class="o">=</span><span class="kt">c</span><span class="p">(</span><span class="s">&quot;-n&quot;</span><span class="p">,</span> <span class="kp">as.character</span><span class="p">(</span>niceness<span class="p">),</span> <span class="kp">Sys.getpid</span><span class="p">()))</span>
<span class="p">}</span>

makeNiceCluster <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>
  cl <span class="o">&lt;-</span> makeCluster<span class="p">(</span><span class="kc">...</span><span class="p">)</span>
  clusterCall<span class="p">(</span>cl<span class="p">,</span> renice.self<span class="p">)</span>
  cl
<span class="p">}</span>

select.nearest <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>x<span class="p">,</span> y<span class="p">)</span> <span class="p">{</span>
  y<span class="p">[</span>nearest<span class="p">(</span>x<span class="p">,</span>y<span class="p">)]</span>
<span class="p">}</span>

kgxref <span class="o">&lt;-</span> get.ucsc.table<span class="p">(</span><span class="s">&quot;knownGene&quot;</span><span class="p">,</span><span class="s">&quot;kgXref&quot;</span><span class="p">)</span>
get.kgxref <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>kgID<span class="p">)</span> <span class="p">{</span>
  x <span class="o">&lt;-</span> <span class="kp">merge</span><span class="p">(</span>x<span class="o">=</span>DataFrame<span class="p">(</span>kgID<span class="o">=</span>kgID<span class="p">),</span> y<span class="o">=</span>kgxref<span class="p">,</span>
             all.x<span class="o">=</span><span class="kc">TRUE</span><span class="p">,</span> all.y<span class="o">=</span><span class="kc">FALSE</span><span class="p">)</span>
  x<span class="p">[</span><span class="kp">names</span><span class="p">(</span>x<span class="p">)</span> <span class="o">!=</span> <span class="s">&quot;kgID&quot;</span><span class="p">]</span>
<span class="p">}</span>

read.htseq.counts <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>f<span class="p">)</span> <span class="p">{</span>
  x <span class="o">&lt;-</span> read.table<span class="p">(</span>f<span class="p">,</span> header<span class="o">=</span><span class="kc">FALSE</span><span class="p">,</span> sep<span class="o">=</span><span class="s">&quot;\t&quot;</span><span class="p">)</span>
  <span class="kp">names</span><span class="p">(</span>x<span class="p">)</span> <span class="o">&lt;-</span> <span class="kt">c</span><span class="p">(</span><span class="s">&quot;ID&quot;</span><span class="p">,</span> <span class="s">&quot;count&quot;</span><span class="p">)</span>
  <span class="c1">## Discard the last 5 lines</span>
  exception.rows <span class="o">&lt;-</span> <span class="p">(</span><span class="kp">nrow</span><span class="p">(</span>x<span class="p">)</span><span class="m">-4</span><span class="p">)</span><span class="o">:</span><span class="kp">nrow</span><span class="p">(</span>x<span class="p">)</span>
  <span class="kp">attr</span><span class="p">(</span>x<span class="p">,</span> <span class="s">&quot;exception_counts&quot;</span><span class="p">)</span> <span class="o">&lt;-</span> x<span class="p">[</span>exception.rows<span class="p">,]</span>
  x <span class="o">&lt;-</span> x<span class="p">[</span><span class="o">-</span>exception.rows<span class="p">,]</span>
  x
<span class="p">}</span>

get.transcript.lengths <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>transcript.ids<span class="p">,</span> exon.lengths<span class="p">)</span> <span class="p">{</span>
  exons.by.transcript <span class="o">&lt;-</span> <span class="kp">split</span><span class="p">(</span>exon.lengths<span class="p">,</span> transcript.ids<span class="p">)</span>
  <span class="kp">sapply</span><span class="p">(</span>exons.by.transcript<span class="p">,</span> <span class="kp">sum</span><span class="p">)</span>
<span class="p">}</span>

get.gene.lengths <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>gene.ids<span class="p">,</span> transcript.lengths<span class="p">,</span> method<span class="o">=</span><span class="s">&quot;max&quot;</span><span class="p">)</span> <span class="p">{</span>
  <span class="kr">if</span> <span class="p">(</span><span class="kp">is.character</span><span class="p">(</span>method<span class="p">))</span> <span class="p">{</span>
    method <span class="o">&lt;-</span> <span class="kp">get</span><span class="p">(</span>method<span class="p">)</span>
  <span class="p">}</span>
  transcripts.by.genes <span class="o">&lt;-</span> <span class="kp">split</span><span class="p">(</span>transcript.lengths<span class="p">,</span> gene.ids<span class="p">)</span>
  <span class="kp">sapply</span><span class="p">(</span>transcripts.by.genes<span class="p">,</span> method<span class="p">)</span>
<span class="p">}</span>

str_matches <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>string<span class="p">,</span> pattern<span class="p">)</span> <span class="p">{</span>
  <span class="o">!</span><span class="kp">is.na</span><span class="p">(</span>str_match<span class="p">(</span>string<span class="p">,</span> pattern<span class="p">)[,</span><span class="m">1</span><span class="p">])</span>
<span class="p">}</span>

annotate.ensp.in.hsap.or.mmul <span class="o">&lt;-</span> <span class="kr">function</span><span class="p">(</span>ensp.ids<span class="p">)</span> <span class="p">{</span>
  ensembl<span class="o">=</span>useMart<span class="p">(</span><span class="s">&quot;ensembl&quot;</span><span class="p">)</span>
  datasets <span class="o">&lt;-</span> <span class="kt">c</span><span class="p">(</span><span class="s">&quot;mmulatta_gene_ensembl&quot;</span><span class="p">,</span> <span class="s">&quot;hsapiens_gene_ensembl&quot;</span><span class="p">)</span>
  x <span class="o">&lt;-</span> <span class="kp">Reduce</span><span class="p">(</span><span class="kp">rbind</span><span class="p">,</span> llply<span class="p">(</span>datasets<span class="p">,</span> <span class="kr">function</span><span class="p">(</span>x<span class="p">)</span> <span class="p">{</span>
    ensembl <span class="o">&lt;-</span> useDataset<span class="p">(</span>x<span class="p">,</span> mart<span class="o">=</span>ensembl<span class="p">)</span>
    getBM<span class="p">(</span>filters<span class="o">=</span><span class="s">&quot;ensembl_peptide_id&quot;</span><span class="p">,</span>
          values<span class="o">=</span><span class="kp">unique</span><span class="p">(</span>ensp.ids<span class="p">),</span>
          attributes<span class="o">=</span><span class="kt">c</span><span class="p">(</span><span class="s">&quot;hgnc_symbol&quot;</span><span class="p">,</span> <span class="s">&quot;wikigene_name&quot;</span><span class="p">,</span> <span class="s">&quot;ensembl_gene_id&quot;</span><span class="p">,</span> <span class="s">&quot;ensembl_transcript_id&quot;</span><span class="p">,</span> <span class="s">&quot;ensembl_peptide_id&quot;</span><span class="p">,</span> <span class="s">&quot;description&quot;</span><span class="p">,</span> <span class="s">&quot;wikigene_description&quot;</span><span class="p">),</span>
          mart<span class="o">=</span>ensembl<span class="p">,</span>
          uniqueRows<span class="o">=</span><span class="kc">TRUE</span><span class="p">)</span>
  <span class="p">}))</span>
  <span class="c1">## Convert empty string to NA in all columns</span>
  x <span class="o">&lt;-</span> <span class="kt">data.frame</span><span class="p">(</span>llply<span class="p">(</span>x<span class="p">,</span> <span class="kr">function</span><span class="p">(</span>column<span class="p">)</span> <span class="kp">ifelse</span><span class="p">(</span>column <span class="o">==</span> <span class="s">&quot;&quot;</span><span class="p">,</span> <span class="kc">NA</span><span class="p">,</span> column<span class="p">)))</span>

  <span class="c1">## Unify symbols &amp; descriptions</span>
  unified.symbol <span class="o">&lt;-</span> <span class="kp">ifelse</span><span class="p">(</span><span class="kp">is.na</span><span class="p">(</span>x<span class="o">$</span>hgnc_symbol<span class="p">),</span> <span class="kp">as.character</span><span class="p">(</span>x<span class="o">$</span>wikigene_name<span class="p">),</span> <span class="kp">as.character</span><span class="p">(</span>x<span class="o">$</span>hgnc_symbol<span class="p">))</span>
  unified.desc <span class="o">&lt;-</span> <span class="kp">ifelse</span><span class="p">(</span><span class="kp">is.na</span><span class="p">(</span>x<span class="o">$</span>description<span class="p">),</span> <span class="kp">as.character</span><span class="p">(</span>x<span class="o">$</span>wikigene_description<span class="p">),</span> <span class="kp">as.character</span><span class="p">(</span>x<span class="o">$</span>description<span class="p">))</span>
  x <span class="o">&lt;-</span> <span class="kt">data.frame</span><span class="p">(</span>symbol<span class="o">=</span>unified.symbol<span class="p">,</span> x<span class="p">[</span><span class="o">!</span> <span class="kp">names</span><span class="p">(</span>x<span class="p">)</span> <span class="o">%in%</span> <span class="kt">c</span><span class="p">(</span><span class="s">&quot;hgnc_symbol&quot;</span><span class="p">,</span> <span class="s">&quot;wikigene_name&quot;</span><span class="p">,</span> <span class="s">&quot;description&quot;</span><span class="p">,</span> <span class="s">&quot;wikigene_description&quot;</span><span class="p">)],</span> description<span class="o">=</span>unified.desc<span class="p">)</span>

  <span class="c1">## Reorder rows so that more-preferred rows for the same input are on top</span>
  x <span class="o">&lt;-</span> x<span class="p">[</span><span class="kp">order</span><span class="p">(</span><span class="kp">is.na</span><span class="p">(</span>x<span class="o">$</span>symbol<span class="p">),</span> str_matches<span class="p">(</span>x<span class="o">$</span>symbol<span class="p">,</span> <span class="s">&quot;^LOC\\d+$&quot;</span><span class="p">),</span> <span class="kp">is.na</span><span class="p">(</span>x<span class="o">$</span>description<span class="p">)),]</span>

  <span class="c1">## Keep only the first row for each input</span>
  x <span class="o">&lt;-</span> x<span class="p">[</span><span class="o">!</span><span class="kp">duplicated</span><span class="p">(</span>x<span class="o">$</span>ensembl_peptide_id<span class="p">),]</span>

  <span class="kt">data.frame</span><span class="p">(</span>x<span class="p">,</span> row.names<span class="o">=</span>x<span class="o">$</span>ensembl_peptide_id<span class="p">)</span>
<span class="p">}</span>

<span class="c1">## TODO: Replace by biomart</span>

CE.name.annot <span class="o">&lt;-</span> <span class="p">{</span>
  x <span class="o">&lt;-</span> setNames<span class="p">(</span>nm<span class="o">=</span><span class="kt">c</span><span class="p">(</span><span class="s">&quot;CE_ensembl_peptide_id&quot;</span><span class="p">,</span> <span class="s">&quot;symbol&quot;</span><span class="p">,</span> <span class="s">&quot;description&quot;</span><span class="p">),</span>
                read.table<span class="p">(</span><span class="s">&quot;annotation/CE.name&quot;</span><span class="p">,</span> sep<span class="o">=</span><span class="s">&quot;\t&quot;</span><span class="p">,</span> quote<span class="o">=</span><span class="s">&quot;&quot;</span><span class="p">))</span>
  x<span class="o">$</span>ensembl_peptide_id <span class="o">&lt;-</span> str_replace<span class="p">(</span>x<span class="o">$</span>CE_ensembl_peptide_id<span class="p">,</span> <span class="s">&quot;^CE_&quot;</span><span class="p">,</span> <span class="s">&quot;&quot;</span><span class="p">)</span>
  <span class="kp">row.names</span><span class="p">(</span>x<span class="p">)</span> <span class="o">&lt;-</span> x<span class="o">$</span>ensembl_peptide_id
  x
<span class="p">}</span>

annotation.gff <span class="o">&lt;-</span> import<span class="p">(</span><span class="s">&quot;cuffmerge_results/merged.gff&quot;</span><span class="p">)</span>

transcripts <span class="o">&lt;-</span> annotation.gff<span class="p">[</span>annotation.gff<span class="o">$</span>type <span class="o">==</span> <span class="s">&quot;transcript&quot;</span><span class="p">,</span> <span class="p">]</span>
exons <span class="o">&lt;-</span> annotation.gff<span class="p">[</span>annotation.gff<span class="o">$</span>type <span class="o">==</span> <span class="s">&quot;exon&quot;</span><span class="p">,</span> <span class="p">]</span>
transcript.lengths <span class="o">&lt;-</span> get.transcript.lengths<span class="p">(</span><span class="kp">unlist</span><span class="p">(</span>exons<span class="o">$</span>Parent<span class="p">),</span> width<span class="p">(</span>exons<span class="p">))</span>
gene.lengths <span class="o">&lt;-</span> get.gene.lengths<span class="p">(</span>transcripts<span class="o">$</span>geneID<span class="p">,</span> transcript.lengths<span class="p">[</span>transcripts<span class="o">$</span>ID<span class="p">])</span>

gene.ref.lists <span class="o">&lt;-</span> <span class="kp">sapply</span><span class="p">(</span><span class="kp">split</span><span class="p">(</span>transcripts<span class="o">$</span>nearest_ref<span class="p">,</span> transcripts<span class="o">$</span>geneID<span class="p">),</span>
                         <span class="kr">function</span><span class="p">(</span>x<span class="p">)</span> <span class="kp">unique</span><span class="p">(</span>x<span class="p">[</span><span class="o">!</span><span class="kp">is.na</span><span class="p">(</span>x<span class="p">)]))</span>

<span class="c1">## For genes with multiple ref IDs, join them with commas</span>
gene.refs <span class="o">&lt;-</span> <span class="kp">sapply</span><span class="p">(</span>gene.ref.lists<span class="p">,</span> <span class="kr">function</span> <span class="p">(</span>x<span class="p">)</span> <span class="p">{</span>
  <span class="kr">if</span> <span class="p">(</span><span class="kp">length</span><span class="p">(</span>x<span class="p">)</span> <span class="o">==</span> <span class="m">0</span><span class="p">)</span> <span class="p">{</span>
    <span class="kc">NA</span>
  <span class="p">}</span> <span class="kr">else</span> <span class="p">{</span>
    str_c<span class="p">(</span>x<span class="p">,</span> collapse<span class="o">=</span><span class="s">&quot;,&quot;</span><span class="p">)</span>
  <span class="p">}</span>
<span class="p">})</span>

<span class="c1">## For genes with multiple ref IDs, just pick the first one</span>
gene.first.refs <span class="o">&lt;-</span> <span class="kp">sapply</span><span class="p">(</span>gene.ref.lists<span class="p">,</span> <span class="kr">function</span><span class="p">(</span>x<span class="p">)</span> <span class="p">{</span>
  <span class="kr">if</span> <span class="p">(</span><span class="kp">length</span><span class="p">(</span>x<span class="p">)</span> <span class="o">==</span> <span class="m">0</span><span class="p">)</span> <span class="p">{</span>
    <span class="kc">NA</span>
  <span class="p">}</span> <span class="kr">else</span> <span class="p">{</span>
    x<span class="p">[[</span><span class="m">1</span><span class="p">]]</span>
  <span class="p">}</span>
<span class="p">})</span>

<span class="c1">## Use delayed assignment so that the cluster won&#39;t be created until it is actually needed</span>
<span class="kp">delayedAssign</span><span class="p">(</span><span class="s">&quot;cl&quot;</span><span class="p">,</span> makeNiceCluster<span class="p">(</span><span class="kp">rep</span><span class="p">(</span><span class="kt">c</span><span class="p">(</span><span class="s">&quot;salomon14&quot;</span><span class="p">,</span> <span class="s">&quot;salomon18&quot;</span><span class="p">,</span> <span class="s">&quot;salomon19&quot;</span><span class="p">),</span> <span class="m">8</span><span class="p">)))</span>

mart.raw.annot <span class="o">&lt;-</span> annotate.ensp.in.hsap.or.mmul<span class="p">(</span>na.omit<span class="p">(</span>gene.first.refs<span class="p">))</span>
gene.annot <span class="o">&lt;-</span> <span class="kt">data.frame</span><span class="p">(</span>mart.raw.annot<span class="p">[</span>gene.first.refs<span class="p">,],</span> row.names<span class="o">=</span><span class="kp">names</span><span class="p">(</span>gene.first.refs<span class="p">))</span>

<span class="c1">## Fill in missing values that are available from the CE.name file</span>
<span class="c1">## provided by the cyno genome paper authors</span>
suppl.gene.annot <span class="o">&lt;-</span> <span class="kt">data.frame</span><span class="p">(</span>CE.name.annot<span class="p">[</span>gene.first.refs<span class="p">,],</span> row.names<span class="o">=</span><span class="kp">names</span><span class="p">(</span>gene.first.refs<span class="p">))</span>

suppl.ensp <span class="o">&lt;-</span> <span class="kp">is.na</span><span class="p">(</span>gene.annot<span class="o">$</span>ensembl_peptide_id<span class="p">)</span> <span class="o">&amp;</span> <span class="o">!</span><span class="kp">is.na</span><span class="p">(</span>suppl.gene.annot<span class="o">$</span>ensembl_peptide_id<span class="p">)</span>
suppl.symbols <span class="o">&lt;-</span> <span class="kp">is.na</span><span class="p">(</span>gene.annot<span class="o">$</span>symbol<span class="p">)</span> <span class="o">&amp;</span> <span class="o">!</span><span class="kp">is.na</span><span class="p">(</span>suppl.gene.annot<span class="o">$</span>symbol<span class="p">)</span>
gene.annot<span class="o">$</span>ensembl_peptide_id <span class="o">&lt;-</span> <span class="kp">ifelse</span><span class="p">(</span>suppl.ensp<span class="p">,</span>
                                        <span class="kp">as.character</span><span class="p">(</span>suppl.gene.annot<span class="o">$</span>ensembl_peptide_id<span class="p">),</span>
                                        <span class="kp">as.character</span><span class="p">(</span>gene.annot<span class="o">$</span>ensembl_peptide_id<span class="p">))</span>
gene.annot<span class="o">$</span>symbol <span class="o">&lt;-</span> <span class="kp">ifelse</span><span class="p">(</span>suppl.symbols<span class="p">,</span>
                            <span class="kp">as.character</span><span class="p">(</span>suppl.gene.annot<span class="o">$</span>symbol<span class="p">),</span>
                            <span class="kp">as.character</span><span class="p">(</span>gene.annot<span class="o">$</span>symbol<span class="p">))</span>
<span class="c1">## Replace description whenever we replace the symbol to keep things consistent</span>
gene.annot<span class="o">$</span>description <span class="o">&lt;-</span> <span class="kp">ifelse</span><span class="p">(</span>suppl.symbols<span class="p">,</span>
                            <span class="kp">as.character</span><span class="p">(</span>suppl.gene.annot<span class="o">$</span>description<span class="p">),</span>
                            <span class="kp">as.character</span><span class="p">(</span>gene.annot<span class="o">$</span>description<span class="p">))</span>
gene.annot<span class="o">$</span>symbol<span class="p">[</span><span class="kp">is.na</span><span class="p">(</span>gene.annot<span class="o">$</span>ensembl_peptide_id<span class="p">)]</span> <span class="o">&lt;-</span> <span class="s">&quot;[No annotation]&quot;</span>
gene.annot<span class="o">$</span>symbol<span class="p">[</span><span class="kp">is.na</span><span class="p">(</span>gene.annot<span class="o">$</span>symbol<span class="p">)]</span> <span class="o">&lt;-</span> <span class="s">&quot;[No symbol for ENSP]&quot;</span>

expdata <span class="o">&lt;-</span> <span class="p">{</span>
  x <span class="o">&lt;-</span> read.xlsx<span class="p">(</span><span class="s">&quot;kenyon-cyno-expdata.xls&quot;</span><span class="p">,</span> <span class="m">1</span><span class="p">)</span>
  x<span class="o">$</span>Animal.ID <span class="o">&lt;-</span> str_trim<span class="p">(</span>x<span class="o">$</span>Animal.ID<span class="p">)</span>
  x<span class="o">$</span>Condition <span class="o">&lt;-</span> str_replace_all<span class="p">(</span>x<span class="o">$</span>Condition<span class="p">,</span> <span class="s">&quot;γ&quot;</span><span class="p">,</span> <span class="s">&quot;g&quot;</span><span class="p">)</span>
  x<span class="o">$</span>Sample.ID <span class="o">&lt;-</span>
    <span class="kp">sprintf</span><span class="p">(</span><span class="s">&quot;%s_%s_%s&quot;</span><span class="p">,</span>
            str_replace_all<span class="p">(</span>x<span class="o">$</span>Animal.ID<span class="p">,</span> <span class="s">&quot;[ -]&quot;</span><span class="p">,</span> <span class="s">&quot;_&quot;</span><span class="p">),</span>
            <span class="kp">ifelse</span><span class="p">(</span>x<span class="o">$</span>Condition <span class="o">==</span> <span class="s">&quot;Control&quot;</span><span class="p">,</span> <span class="s">&quot;CTRL&quot;</span><span class="p">,</span> <span class="s">&quot;IFNg&quot;</span><span class="p">),</span>
            x<span class="o">$</span>Passage<span class="p">)</span>
  x<span class="o">$</span>Sample.Name <span class="o">&lt;-</span>
    <span class="kp">sprintf</span><span class="p">(</span><span class="s">&quot;%s_%s_%s_L%03i&quot;</span><span class="p">,</span>
            str_replace_all<span class="p">(</span>x<span class="o">$</span>Animal.ID<span class="p">,</span> <span class="s">&quot;[ -]&quot;</span><span class="p">,</span> <span class="s">&quot;_&quot;</span><span class="p">),</span>
            <span class="kp">ifelse</span><span class="p">(</span>x<span class="o">$</span>Condition <span class="o">==</span> <span class="s">&quot;Control&quot;</span><span class="p">,</span> <span class="m">1</span><span class="p">,</span> <span class="m">2</span><span class="p">),</span>
            x<span class="o">$</span>Index.Seq<span class="p">,</span>
            x<span class="o">$</span>Lane<span class="p">)</span>
  x<span class="o">$</span>FASTQ.Read1.File <span class="o">&lt;-</span> <span class="kp">sprintf</span><span class="p">(</span><span class="s">&quot;seqprep_results/%s/%s_R1_001.fastq&quot;</span><span class="p">,</span> x<span class="o">$</span>Sample.Name<span class="p">,</span> x<span class="o">$</span>Sample.Name<span class="p">)</span>
  x<span class="o">$</span>FASTQ.Read2.File <span class="o">&lt;-</span> <span class="kp">sprintf</span><span class="p">(</span><span class="s">&quot;seqprep_results/%s/%s_R2_001.fastq&quot;</span><span class="p">,</span> x<span class="o">$</span>Sample.Name<span class="p">,</span> x<span class="o">$</span>Sample.Name<span class="p">)</span>
  x<span class="o">$</span>BAM.File <span class="o">&lt;-</span> <span class="kp">sprintf</span><span class="p">(</span><span class="s">&quot;tophat_results/%s/accepted_hits.bam&quot;</span><span class="p">,</span> x<span class="o">$</span>Sample.Name<span class="p">)</span>
  x<span class="o">$</span>GFF.File <span class="o">&lt;-</span> <span class="kp">sprintf</span><span class="p">(</span><span class="s">&quot;cufflinks_quantification/%s/transcripts.gff&quot;</span><span class="p">,</span> x<span class="o">$</span>Sample.Name<span class="p">)</span>
  x<span class="o">$</span>Counts.File <span class="o">&lt;-</span> <span class="kp">sprintf</span><span class="p">(</span><span class="s">&quot;htseq_counts/%s/counts.txt&quot;</span><span class="p">,</span> x<span class="o">$</span>Sample.Name<span class="p">)</span>
  mcparallel<span class="p">(</span>write.xlsx<span class="p">(</span>x<span class="p">,</span> <span class="s">&quot;expdata.xlsx&quot;</span><span class="p">))</span>
  <span class="kp">rownames</span><span class="p">(</span>x<span class="p">)</span> <span class="o">&lt;-</span> x<span class="o">$</span>Sample.ID
  x
<span class="p">}</span>

counts.vectors <span class="o">&lt;-</span> setNames<span class="p">(</span>llply<span class="p">(</span>expdata<span class="o">$</span>Counts.File<span class="p">,</span> <span class="m">.</span>parallel<span class="o">=</span><span class="kc">TRUE</span><span class="p">,</span> <span class="kr">function</span><span class="p">(</span>f<span class="p">)</span> <span class="p">{</span>
  x <span class="o">&lt;-</span> read.htseq.counts<span class="p">(</span>f<span class="p">)</span>
  setNames<span class="p">(</span>x<span class="o">$</span>count<span class="p">,</span> x<span class="o">$</span>ID<span class="p">)</span>
<span class="p">}),</span> expdata<span class="o">$</span>Sample.ID<span class="p">)</span>

<span class="c1">## Put the data into a matrix, making sure we account for the</span>
<span class="c1">## possibility that not all genes are listed in all samples.</span>
all.geneIDs <span class="o">&lt;-</span> <span class="kp">sort</span><span class="p">(</span><span class="kp">unique</span><span class="p">(</span><span class="kp">unlist</span><span class="p">(</span>llply<span class="p">(</span>counts.vectors<span class="p">,</span> <span class="kp">names</span><span class="p">))))</span>

counts <span class="o">&lt;-</span> <span class="p">{</span>
  x <span class="o">&lt;-</span> <span class="kt">matrix</span><span class="p">(</span>data<span class="o">=</span><span class="m">0</span><span class="p">,</span> ncol<span class="o">=</span><span class="kp">length</span><span class="p">(</span>counts.vectors<span class="p">),</span> nrow<span class="o">=</span><span class="kp">length</span><span class="p">(</span>all.geneIDs<span class="p">),</span>
              dimnames<span class="o">=</span><span class="kt">list</span><span class="p">(</span><span class="sb">`geneID`</span><span class="o">=</span>all.geneIDs<span class="p">,</span> <span class="sb">`sample`</span><span class="o">=</span><span class="kp">names</span><span class="p">(</span>counts.vectors<span class="p">)))</span>
  <span class="kr">for</span> <span class="p">(</span>i <span class="kr">in</span> expdata<span class="o">$</span>Sample.ID<span class="p">)</span> <span class="p">{</span>
    cvec <span class="o">&lt;-</span> counts.vectors<span class="p">[[</span>i<span class="p">]]</span>
    x<span class="p">[</span><span class="kp">names</span><span class="p">(</span>cvec<span class="p">),</span>i<span class="p">]</span> <span class="o">&lt;-</span> <span class="kp">cbind</span><span class="p">(</span>cvec<span class="p">)</span>
  <span class="p">}</span>
  x
<span class="p">}</span>

blocked.design <span class="o">&lt;-</span> model.matrix<span class="p">(</span><span class="o">~</span>Animal.ID<span class="o">+</span>Passage<span class="o">+</span>Condition<span class="p">,</span> data<span class="o">=</span>expdata<span class="p">)</span>
unblocked.design <span class="o">&lt;-</span> model.matrix<span class="p">(</span><span class="o">~</span>Condition<span class="p">,</span> data<span class="o">=</span>expdata<span class="p">)</span>
dge <span class="o">&lt;-</span> DGEList<span class="p">(</span>counts<span class="o">=</span>counts<span class="p">,</span>
               group<span class="o">=</span>expdata<span class="o">$</span>Condition<span class="p">,</span>
               genes<span class="o">=</span>gene.annot<span class="p">[</span><span class="kp">rownames</span><span class="p">(</span>counts<span class="p">),])</span>
dge <span class="o">&lt;-</span> calcNormFactors<span class="p">(</span>dge<span class="p">)</span>

blocked.dge <span class="o">&lt;-</span> estimateGLMCommonDisp<span class="p">(</span>dge<span class="p">,</span> blocked.design<span class="p">,</span> verbose<span class="o">=</span><span class="kc">TRUE</span><span class="p">)</span>
blocked.dge <span class="o">&lt;-</span> estimateGLMTrendedDisp<span class="p">(</span>blocked.dge<span class="p">,</span> blocked.design<span class="p">)</span>
blocked.dge <span class="o">&lt;-</span> estimateGLMTagwiseDisp<span class="p">(</span>blocked.dge<span class="p">,</span> blocked.design<span class="p">)</span>
blocked.fit <span class="o">&lt;-</span> glmFit<span class="p">(</span>blocked.dge<span class="p">,</span> blocked.design<span class="p">)</span>
blocked.lrt <span class="o">&lt;-</span> glmLRT<span class="p">(</span>blocked.dge<span class="p">,</span> blocked.fit<span class="p">,</span> coef<span class="o">=</span><span class="s">&quot;ConditionIFNg activated&quot;</span><span class="p">)</span>
blocked.tt <span class="o">&lt;-</span> topTags<span class="p">(</span>blocked.lrt<span class="p">,</span> n<span class="o">=</span><span class="kp">nrow</span><span class="p">(</span>counts<span class="p">))</span>

unblocked.dge <span class="o">&lt;-</span> estimateGLMCommonDisp<span class="p">(</span>dge<span class="p">,</span> unblocked.design<span class="p">,</span> verbose<span class="o">=</span><span class="kc">TRUE</span><span class="p">)</span>
unblocked.dge <span class="o">&lt;-</span> estimateGLMTrendedDisp<span class="p">(</span>unblocked.dge<span class="p">,</span> unblocked.design<span class="p">)</span>
unblocked.dge <span class="o">&lt;-</span> estimateGLMTagwiseDisp<span class="p">(</span>unblocked.dge<span class="p">,</span> unblocked.design<span class="p">)</span>
unblocked.fit <span class="o">&lt;-</span> glmFit<span class="p">(</span>unblocked.dge<span class="p">,</span> unblocked.design<span class="p">)</span>
unblocked.lrt <span class="o">&lt;-</span> glmLRT<span class="p">(</span>unblocked.dge<span class="p">,</span> unblocked.fit<span class="p">,</span> coef<span class="o">=</span><span class="s">&quot;ConditionIFNg activated&quot;</span><span class="p">)</span>
unblocked.tt <span class="o">&lt;-</span> topTags<span class="p">(</span>unblocked.lrt<span class="p">,</span> n<span class="o">=</span><span class="kp">nrow</span><span class="p">(</span>counts<span class="p">))</span>

write.csv<span class="p">(</span>blocked.tt<span class="o">$</span><span class="kp">table</span><span class="p">,</span> <span class="s">&quot;edgeR-genes-prelim&quot;</span><span class="p">)</span>
write.xlsx.multisheet<span class="p">(</span><span class="kt">list</span><span class="p">(</span>blocked<span class="o">=</span>blocked.tt<span class="o">$</span><span class="kp">table</span><span class="p">,</span>
                           unblocked<span class="o">=</span>unblocked.tt<span class="o">$</span><span class="kp">table</span><span class="p">),</span>
                      <span class="s">&quot;edgeR-genes.xlsx&quot;</span><span class="p">)</span>
</pre></div>
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