Mercurial > repos > yhoogstrate > edger_with_design_matrix
annotate edgeR_Differential_Gene_Expression.xml @ 106:56117c9db713 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
author | yhoogstrate |
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date | Tue, 01 Sep 2015 04:25:37 -0400 |
parents | f2ac9f6bc542 |
children | 049d8bc2214e |
rev | line source |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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1 <?xml version="1.0" encoding="UTF-8"?> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.a"> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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4 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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5 <requirements> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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6 <requirement type="package" version="3.11.0">edger</requirement> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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7 </requirements> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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8 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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9 <stdio> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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10 <regex match="Error in[^a-z]+contrasts" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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11 source="both" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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12 level="fatal" |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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13 description="Have the design- and expression-matrix been swapped?" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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14 <regex match="Execution halted" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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15 source="both" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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16 level="fatal" /> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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17 <regex match="Calculating library sizes from column" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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18 source="stderr" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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19 level="log" /> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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20 <regex match="During startup - Warning messages" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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21 source="stderr" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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22 level="log" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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23 <regex match="Setting LC_[^ ]+ failed" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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24 source="stderr" |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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25 level="warning" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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26 description="LOCALE has not been set correctly" /> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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27 </stdio> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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28 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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29 <version_command>echo $(R --version | grep version | grep -v GNU) " , EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")</version_command> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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30 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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31 <command> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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32 <!-- |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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33 The following script is written in the "Cheetah" language: |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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34 http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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35 --> |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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36 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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37 R --vanilla --slave -f $R_script '--args |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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38 $expression_matrix |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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39 $design_matrix |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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40 $contrast |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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41 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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42 $fdr |
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43 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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44 $output_count_edgeR |
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45 $output_cpm |
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46 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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47 /dev/null <!-- Calculation of FPKM/RPKM should come here --> |
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48 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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49 #if $output_raw_counts: |
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50 $output_raw_counts |
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51 #else: |
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52 /dev/null |
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53 #end if |
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54 |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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55 #if $output_MDSplot_logFC: |
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56 $output_MDSplot_logFC |
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57 #else: |
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58 /dev/null |
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59 #end if |
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60 |
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61 #if $output_MDSplot_bcv: |
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62 $output_MDSplot_bcv |
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63 #else: |
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64 /dev/null |
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65 #end if |
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66 |
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67 #if $output_BCVplot: |
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68 $output_BCVplot |
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69 #else: |
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70 /dev/null |
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71 #end if |
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72 |
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73 #if $output_MAplot: |
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74 $output_MAplot |
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75 #else: |
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76 /dev/null |
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77 #end if |
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78 |
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79 #if $output_PValue_distribution_plot: |
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80 $output_PValue_distribution_plot |
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81 #else: |
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82 /dev/null |
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83 #end if |
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84 |
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85 #if $output_hierarchical_clustering_plot: |
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86 $output_hierarchical_clustering_plot |
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87 #else: |
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88 /dev/null |
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89 #end if |
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90 |
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91 #if $output_heatmap_plot: |
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92 $output_heatmap_plot |
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93 #else: |
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94 /dev/null |
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95 #end if |
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96 |
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97 #if $output_RData_obj: |
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98 $output_RData_obj |
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99 #else: |
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100 /dev/null |
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101 #end if |
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102 |
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103 $output_format_images |
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104 ' |
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105 #if $output_R: |
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106 > $output_R |
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107 #else: |
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108 > /dev/null |
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109 #end if |
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110 </command> |
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111 |
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112 <configfiles> |
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113 <configfile name="R_script"> |
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114 library(limma,quietly=TRUE) ## enable quietly to avoid unnecessaity stderr dumping |
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115 library(edgeR,quietly=TRUE) ## enable quietly to avoid unnecessaity stderr dumping |
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116 library(splines,quietly=TRUE) ## enable quietly to avoid unnecessaity stderr dumping |
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117 |
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118 ## Fetch commandline arguments |
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119 args <- commandArgs(trailingOnly = TRUE) |
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120 |
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121 expression_matrix_file = args[1] |
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122 design_matrix_file = args[2] |
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123 contrast = args[3] |
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124 |
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125 fdr = args[4] |
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126 |
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127 output_count_edgeR = args[5] |
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128 output_cpm = args[6] |
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129 |
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130 output_xpkm = args[7] ##FPKM file - yet to be implemented |
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131 |
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132 output_raw_counts = args[8] |
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133 output_MDSplot_logFC = args[9] |
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134 output_MDSplot_bcv = args[10] |
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135 output_BCVplot = args[11] |
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136 output_MAplot = args[12] |
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137 output_PValue_distribution_plot = args[13] |
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138 output_hierarchical_clustering_plot = args[14] |
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139 output_heatmap_plot = args[15] |
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140 output_RData_obj = args[16] |
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141 output_format_images = args[17] |
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142 |
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143 |
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144 library(edgeR) |
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145 ##raw_data <- read.delim(designmatrix,header=T,stringsAsFactors=T) |
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146 ## Obtain read-counts |
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147 |
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148 expression_matrix <- read.delim(expression_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c("")) |
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149 design_matrix <- read.delim(design_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c("")) |
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150 |
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151 colnames(design_matrix) <- make.names(colnames(design_matrix)) |
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152 |
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153 for(i in 1:ncol(design_matrix)) { |
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154 old <- design_matrix[,i] |
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155 design_matrix[,i] <- make.names(design_matrix[,i]) |
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156 if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) { |
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157 print("Renaming of factors:") |
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158 print(old) |
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159 print("To:") |
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160 print(design_matrix[,i]) |
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161 } |
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162 ## The following line seems to malfunction the script: |
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163 ##design_matrix[,i] <- as.factor(design_matrix[,i]) |
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164 } |
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165 |
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166 ## 1) In the expression matrix, you only want to have the samples described in the design matrix |
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167 columns <- match(rownames(design_matrix),colnames(expression_matrix)) |
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168 columns <- columns[!is.na(columns)] |
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169 read_counts <- expression_matrix[,columns] |
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170 |
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171 ## 2) In the design matrix, you only want to have samples of which you really have the counts |
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172 columns <- match(colnames(read_counts),rownames(design_matrix)) |
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173 columns <- columns[!is.na(columns)] |
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174 design_matrix <- design_matrix[columns,,drop=FALSE] |
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175 |
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176 ## Filter for HTSeq predifined counts: |
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177 exclude_HTSeq <- c("no_feature","ambiguous","too_low_aQual","not_aligned","alignment_not_unique") |
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178 exclude_DEXSeq <- c("_ambiguous","_empty","_lowaqual","_notaligned") |
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179 |
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180 exclude <- match(c(exclude_HTSeq, exclude_DEXSeq),rownames(read_counts)) |
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181 exclude <- exclude[is.na(exclude)==0] |
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182 if(length(exclude) != 0) { |
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183 read_counts <- read_counts[-exclude,] |
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184 } |
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185 |
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186 |
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187 ## sorting expression matrix with the order of the read_counts |
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188 ##order <- match(colnames(read_counts) , rownames(design_matrix)) |
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189 ##read_counts_ordered <- read_counts[,order2] |
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190 |
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191 empty_samples <- apply(read_counts,2,function(x) sum(x) == 0) |
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192 if(sum(empty_samples) > 0) { |
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193 write(paste("There are ",sum(empty_samples)," empty samples found:",sep=""),stderr()) |
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194 write(colnames(read_counts)[empty_samples],stderr()) |
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195 } else { |
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196 |
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197 dge <- DGEList(counts=read_counts,genes=rownames(read_counts)) |
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198 |
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199 formula <- paste(c("~0",make.names(colnames(design_matrix))),collapse = " + ") |
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200 design_matrix_tmp <- design_matrix |
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201 colnames(design_matrix_tmp) <- make.names(colnames(design_matrix_tmp)) |
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202 design <- model.matrix(as.formula(formula),design_matrix_tmp) |
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203 rm(design_matrix_tmp) |
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204 |
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205 # Filter prefixes |
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206 prefixes = colnames(design_matrix)[attr(design,"assign")] |
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207 avoid = nchar(prefixes) == nchar(colnames(design)) |
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208 replacements = substr(colnames(design),nchar(prefixes)+1,nchar(colnames(design))) |
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209 replacements[avoid] = colnames(design)[avoid] |
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210 colnames(design) = replacements |
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211 |
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212 # Do normalization |
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213 write("Calculating normalization factors...",stdout()) |
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214 dge <- calcNormFactors(dge) |
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215 write("Estimating common dispersion...",stdout()) |
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216 dge <- estimateGLMCommonDisp(dge,design) |
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217 write("Estimating trended dispersion...",stdout()) |
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218 dge <- estimateGLMTrendedDisp(dge,design) |
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219 write("Estimating tagwise dispersion...",stdout()) |
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220 dge <- estimateGLMTagwiseDisp(dge,design) |
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221 |
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222 |
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223 if(output_MDSplot_logFC != "/dev/null") { |
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224 write("Creating MDS plot (logFC method)",stdout()) |
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225 points <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot |
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226 dev.off()# Kill it |
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227 |
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228 if(output_format_images == "pdf") { |
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229 pdf(output_MDSplot_logFC,height=14,width=14) |
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230 } else if(output_format_images == "svg") { |
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231 svg(output_MDSplot_logFC,height=14,width=14) |
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232 } else { |
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233 ## png(output_MDSplot_logFC) |
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234 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/ |
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235 |
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236 bitmap(output_MDSplot_logFC,type="png16m",height=14,width=14) |
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237 } |
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238 |
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239 |
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240 diff_x <- abs(max(points\$x)-min(points\$x)) |
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241 diff_y <-(max(points\$y)-min(points\$y)) |
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242 plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2") |
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243 points(points\$x,points\$y,pch=20) |
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244 text(points\$x, points\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) |
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245 rm(diff_x,diff_y) |
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246 |
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247 dev.off() |
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248 } |
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249 |
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250 if(output_MDSplot_bcv != "/dev/null") { |
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251 write("Creating MDS plot (bcv method)",stdout()) |
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252 |
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253 ## 1. First create a virtual plot to obtain the desired coordinates |
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254 pdf("bcvmds.pdf") |
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255 points <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples))) |
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256 dev.off()# Kill it |
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257 |
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258 ## 2. Re-plot the coordinates in a new figure with the size and settings. |
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259 if(output_format_images == "pdf") { |
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260 pdf(output_MDSplot_bcv,height=14,width=14) |
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261 } else if(output_format_images == "svg") { |
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262 svg(output_MDSplot_bcv,height=14,width=14) |
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263 } else { |
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264 ## png(output_MDSplot_bcv) |
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265 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/ |
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266 |
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267 bitmap(output_MDSplot_bcv,type="png16m",height=14,width=14) |
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268 } |
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269 |
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270 diff_x <- abs(max(points\$x)-min(points\$x)) |
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271 diff_y <-(max(points\$y)-min(points\$y)) |
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272 plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2") |
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273 points(points\$x,points\$y,pch=20) |
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274 text(points\$x, points\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) |
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275 rm(diff_x,diff_y) |
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276 |
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277 dev.off() |
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278 } |
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279 |
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280 |
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281 if(output_BCVplot != "/dev/null") { |
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282 write("Creating Biological coefficient of variation plot",stdout()) |
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283 |
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284 if(output_format_images == "pdf") { |
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285 pdf(output_BCVplot) |
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286 } else if(output_format_images == "svg") { |
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287 svg(output_BCVplot) |
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288 } else { |
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289 ## png(output_BCVplot) |
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290 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/ |
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291 |
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292 bitmap(output_BCVplot,type="png16m") |
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293 } |
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294 |
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295 plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance") |
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296 dev.off() |
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297 } |
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298 |
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299 |
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300 write("Fitting GLM...",stdout()) |
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301 fit <- glmFit(dge,design) |
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302 |
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303 write(paste("Performing likelihood ratio test: ",contrast,sep=""),stdout()) |
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304 cont <- c(contrast) |
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305 cont <- makeContrasts(contrasts=cont, levels=design) |
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306 |
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307 lrt <- glmLRT(fit, contrast=cont[,1]) |
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308 write(paste("Exporting to file: ",output_count_edgeR,sep=""),stdout()) |
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309 write.table(file=output_count_edgeR,topTags(lrt,n=nrow(read_counts))\$table,sep="\t",row.names=TRUE,col.names=NA) |
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310 write.table(file=output_cpm,cpm(dge,normalized.lib.sizes=TRUE),sep="\t",row.names=TRUE,col.names=NA) |
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311 |
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312 ## todo EXPORT FPKM |
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313 write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA) |
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314 |
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315 if(output_MAplot != "/dev/null" || output_PValue_distribution_plot != "/dev/null") { |
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316 etable <- topTags(lrt, n=nrow(dge))\$table |
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317 etable <- etable[order(etable\$FDR), ] |
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318 |
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319 if(output_MAplot != "/dev/null") { |
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320 write("Creating MA plot...",stdout()) |
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321 |
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322 if(output_format_images == "pdf") { |
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323 pdf(output_MAplot) |
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324 } else if(output_format_images == "svg") { |
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325 svg(output_MAplot) |
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326 } else { |
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327 ## png(output_MAplot) |
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328 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/ |
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329 |
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330 bitmap(output_MAplot,type="png16m") |
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331 } |
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332 |
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333 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance")) |
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334 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red")) |
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335 abline(h=c(-1,1), col="blue") |
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336 dev.off() |
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337 } |
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338 |
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339 if(output_PValue_distribution_plot != "/dev/null") { |
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340 write("Creating P-value distribution plot...",stdout()) |
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341 |
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342 if(output_format_images == "pdf") { |
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343 pdf(output_PValue_distribution_plot,width=14,height=14) |
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344 } else if(output_format_images == "svg") { |
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345 svg(output_PValue_distribution_plot,width=14,height=14) |
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346 } else { |
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347 ## png(output_PValue_distribution_plot) |
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348 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/ |
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349 |
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350 bitmap(output_PValue_distribution_plot,type="png16m",width=14,height=14) |
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351 } |
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352 |
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353 expressed_genes <- subset(etable, PValue < 0.99) |
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354 h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)") |
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355 center <- sum(h\$counts) / length(h\$counts) |
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356 lines(c(0,1),c(center,center),lty=2,col="red",lwd=2) |
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357 k <- ksmooth(h\$mid, h\$counts) |
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358 lines(k\$x,k\$y,col="red",lwd=2) |
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359 rmsd <- (h\$counts) - center |
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360 rmsd <- rmsd^2 |
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361 rmsd <- sum(rmsd) |
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362 rmsd <- sqrt(rmsd) |
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363 text(0,max(h\$counts),paste("e=",round(rmsd,2),sep=""),pos=4,col="blue") |
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364 ## change e into epsilon somehow |
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365 dev.off() |
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366 } |
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367 } |
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368 |
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369 if(output_heatmap_plot != "/dev/null") { |
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370 |
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371 if(output_format_images == "pdf") { |
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372 pdf(output_heatmap_plot,width=10.5) |
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373 } else if(output_format_images == "svg") { |
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374 svg(output_heatmap_plot,width=10.5) |
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375 } else { |
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376 ## png(output_heatmap_plot) |
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377 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/ |
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378 |
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379 bitmap(output_heatmap_plot,type="png16m",width=10.5) |
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380 } |
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381 |
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382 etable2 <- topTags(lrt, n=100)\$table |
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383 order <- rownames(etable2) |
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384 cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),] |
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385 heatmap(t(cpm_sub)) |
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386 dev.off() |
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387 } |
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388 |
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389 ##output_hierarchical_clustering_plot = args[13] |
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390 |
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391 if(output_RData_obj != "/dev/null") { |
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392 save.image(output_RData_obj) |
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393 } |
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394 |
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395 write("Done!",stdout()) |
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396 } |
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397 </configfile> |
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398 </configfiles> |
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399 |
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400 <inputs> |
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401 <param name="expression_matrix" type="data" format="tabular" label="Expression (read count) matrix" /> |
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402 <param name="design_matrix" type="data" format="tabular" label="Design matrix" help="Ensure your samplenames are identical to those in the expression matrix. Preferentially, create the contrast matrix using 'edgeR: Design- from Expression matrix'." /> |
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403 |
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404 <param name="contrast" type="text" label="Contrast (biological question)" help="e.g. 'tumor-normal' or '(G1+G2)/2-G3' using the factors chosen in the design matrix. Read the 'makeContrasts' manual from Limma package for more info: http://www.bioconductor.org/packages/release/bioc/html/limma.html and http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf." /> |
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405 |
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406 <param name="fdr" type="float" min="0" max="1" value="0.05" label="False Discovery Rate (FDR)" /> |
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407 |
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408 <param name="outputs" type="select" label="Optional desired outputs" multiple="true" display="checkboxes"> |
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409 <option value="make_output_raw_counts">Raw counts table</option> |
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410 <option value="make_output_MDSplot_logFC">MDS-plot (logFC-method)</option> |
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411 <option value="make_output_MDSplot_bcv">MDS-plot (BCV-method; much slower)</option> |
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412 <option value="make_output_BCVplot">BCV-plot</option> |
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413 <option value="make_output_MAplot">MA-plot</option> |
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414 <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option> |
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415 <option value="make_output_hierarchical_clustering_plot">Hierarchical custering (under contstruction)</option> |
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416 <option value="make_output_heatmap_plot">Heatmap</option> |
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417 |
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418 <option value="make_output_R_stdout">R stdout</option> |
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419 <option value="make_output_RData_obj">R Data object</option> |
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420 </param> |
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421 |
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422 <param name="output_format_images" type="select" label="Output format of images" display="radio"> |
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423 <option value="png">Portable network graphics (.png)</option> |
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424 <option value="pdf">Portable document format (.pdf)</option> |
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425 <option value="svg">Scalable vector graphics (.svg)</option> |
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426 </param> |
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|
427 </inputs> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
428 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
429 <outputs> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
430 <data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differentially expressed genes" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
431 <data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
432 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
433 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts"> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
434 <filter>outputs and ("make_output_raw_counts" in outputs)</filter> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
435 </data> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
436 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
437 <data format="png" name="output_MDSplot_logFC" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (logFC method)"> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
438 <filter>outputs and ("make_output_MDSplot_logFC" in outputs)</filter> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
439 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
440 <change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
441 <when input="output_format_images" value="png" format="png" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
442 <when input="output_format_images" value="pdf" format="pdf" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
443 <when input="output_format_images" value="svg" format="svg" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
444 </change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
445 </data> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
446 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
447 <data format="png" name="output_MDSplot_bcv" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (bcv method)"> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
448 <filter>outputs and ("make_output_MDSplot_bcv" in outputs)</filter> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
449 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
450 <change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
451 <when input="output_format_images" value="png" format="png" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
452 <when input="output_format_images" value="pdf" format="pdf" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
453 <when input="output_format_images" value="svg" format="svg" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
454 </change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
455 </data> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
456 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
457 <data format="png" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot"> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
458 <filter>outputs and ("make_output_BCVplot" in outputs)</filter> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
459 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
460 <change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
461 <when input="output_format_images" value="png" format="png" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
462 <when input="output_format_images" value="pdf" format="pdf" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
463 <when input="output_format_images" value="svg" format="svg" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
464 </change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
465 </data> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
466 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
467 <data format="png" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot"> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
468 <filter>outputs and ("make_output_MAplot" in outputs)</filter> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
469 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
470 <change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
471 <when input="output_format_images" value="png" format="png" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
472 <when input="output_format_images" value="pdf" format="pdf" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
473 <when input="output_format_images" value="svg" format="svg" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
474 </change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
475 </data> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
476 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
477 <data format="png" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution"> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
478 <filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
479 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
480 <change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
481 <when input="output_format_images" value="png" format="png" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
482 <when input="output_format_images" value="pdf" format="pdf" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
483 <when input="output_format_images" value="svg" format="svg" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
484 </change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
485 </data> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
486 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
487 <data format="png" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering"> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
488 <filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
489 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
490 <change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
491 <when input="output_format_images" value="png" format="png" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
492 <when input="output_format_images" value="pdf" format="pdf" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
493 <when input="output_format_images" value="svg" format="svg" /> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
494 </change_format> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
495 </data> |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff
changeset
|
496 |
f2ac9f6bc542
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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497 <data format="png" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap"> |
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498 <filter>outputs and ("make_output_heatmap_plot" in outputs)</filter> |
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499 |
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500 <change_format> |
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501 <when input="output_format_images" value="png" format="png" /> |
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502 <when input="output_format_images" value="pdf" format="pdf" /> |
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503 <when input="output_format_images" value="svg" format="svg" /> |
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504 </change_format> |
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505 </data> |
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506 |
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507 <data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object"> |
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508 <filter>outputs and ("make_output_RData_obj" in outputs)</filter> |
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509 </data> |
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510 |
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511 <data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" > |
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512 <filter>outputs and ("make_output_R_stdout" in outputs)</filter> |
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513 </data> |
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514 </outputs> |
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515 |
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516 <tests> |
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517 <test> |
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518 <param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" /> |
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519 <param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.txt" /> |
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520 |
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521 <param name="contrast" value="E-C"/> |
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522 |
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523 <param name="fdr" value="0.05" /> |
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524 |
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525 <param name="output_format_images" value="png" /> |
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526 |
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527 <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.tabular.txt" /> |
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528 </test> |
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529 </tests> |
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530 |
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531 <help> |
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532 edgeR: Differential Gene(Expression) Analysis |
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533 ############################################# |
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534 |
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535 Overview |
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536 -------- |
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537 Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis with other types of genome-scale count data [1]. |
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538 |
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539 For every experiment, the algorithm requires a design matrix. This matrix describes which samples belong to which groups. |
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540 More details on this are given in the edgeR manual: http://www.bioconductor.org/packages/2.12/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf |
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541 and the limma manual. |
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542 |
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543 Because the creation of a design matrix can be complex and time consuming, especially if no GUI is used, this package comes with an alternative tool which can help you with it. |
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544 This tool is called *edgeR Design Matrix Creator*. |
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545 If the appropriate design matrix (with corresponding links to the files) is given, |
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546 the correct contrast ( http://en.wikipedia.org/wiki/Contrast_(statistics) ) has to be given. |
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547 |
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548 If you have for example two groups, with an equal weight, you would like to compare either |
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549 "g1-g2" or "normal-cancer". |
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550 |
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551 The test function makes use of a MCF7 dataset used in a study that indicates that a higher sequencing depth is not neccesairily more important than a higher amount of replaciates[2]. |
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552 |
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553 Input |
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554 ----- |
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555 Expression matrix |
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556 ^^^^^^^^^^^^^^^^^ |
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557 :: |
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558 |
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559 Geneid "\t" Sample-1 "\t" Sample-2 "\t" Sample-3 "\t" Sample-4 [...] "\n" |
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560 SMURF "\t" 123 "\t" 21 "\t" 34545 "\t" 98 ... "\n" |
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561 BRCA1 "\t" 435 "\t" 6655 "\t" 45 "\t" 55 ... "\n" |
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562 LINK33 "\t" 4 "\t" 645 "\t" 345 "\t" 1 ... "\n" |
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563 SNORD78 "\t" 498 "\t" 65 "\t" 98 "\t" 27 ... "\n" |
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564 [...] |
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565 |
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566 *Note: Make sure the number of columns in the header is identical to the number of columns in the body.* |
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567 |
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568 Design matrix |
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569 ^^^^^^^^^^^^^ |
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570 :: |
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571 |
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572 Sample "\t" Condition "\t" Ethnicity "\t" Patient "\t" Batch "\n" |
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573 Sample-1 "\t" Tumor "\t" European "\t" 1 "\t" 1 "\n" |
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574 Sample-2 "\t" Normal "\t" European "\t" 1 "\t" 1 "\n" |
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575 Sample-3 "\t" Tumor "\t" European "\t" 2 "\t" 1 "\n" |
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576 Sample-4 "\t" Normal "\t" European "\t" 2 "\t" 1 "\n" |
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577 Sample-5 "\t" Tumor "\t" African "\t" 3 "\t" 1 "\n" |
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578 Sample-6 "\t" Normal "\t" African "\t" 3 "\t" 1 "\n" |
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579 Sample-7 "\t" Tumor "\t" African "\t" 4 "\t" 2 "\n" |
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580 Sample-8 "\t" Normal "\t" African "\t" 4 "\t" 2 "\n" |
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581 Sample-9 "\t" Tumor "\t" Asian "\t" 5 "\t" 2 "\n" |
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582 Sample-10 "\t" Normal "\t" Asian "\t" 5 "\t" 2 "\n" |
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583 Sample-11 "\t" Tumor "\t" Asian "\t" 6 "\t" 2 "\n" |
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584 Sample-12 "\t" Normal "\t" Asian "\t" 6 "\t" 2 "\n" |
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585 |
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586 *Note: Avoid factor names that are (1) numerical, (2) contain mathematical symbols and preferebly only use letters.* |
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587 |
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588 Contrast |
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589 ^^^^^^^^ |
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590 The contrast represents the biological question. There can be many questions asked, e.g.: |
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591 |
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592 - Tumor-Normal |
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593 - African-European |
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594 - 0.5*(Control+Placebo) / Treated |
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595 |
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596 Installation |
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597 ------------ |
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598 |
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599 This tool requires no specific configurations. The following dependencies are installed automatically: |
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600 |
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601 - R |
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602 - Bioconductor |
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603 - limma |
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604 - edgeR |
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605 |
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606 License |
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607 ------- |
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608 - R |
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609 - GPL 2 & GPL 3 |
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610 - limma |
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611 - GPL (>=2) |
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612 - edgeR |
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613 - GPL (>=2) |
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614 |
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615 References |
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616 ---------- |
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617 |
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618 EdgeR |
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619 ^^^^^ |
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620 **[1] edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.** |
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621 |
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622 *Mark D. Robinson, Davis J. McCarthy and Gordon K. Smyth* - Bioinformatics (2010) 26 (1): 139-140. |
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623 |
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624 - http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html |
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625 - http://dx.doi.org/10.1093/bioinformatics/btp616 |
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626 - http://www.bioconductor.org/packages/release/bioc/html/edgeR.html |
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627 |
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628 Test-data (MCF7) |
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629 ^^^^^^^^^^^^^^^^ |
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630 **[2] RNA-seq differential expression studies: more sequence or more replication?** |
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631 |
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632 *Yuwen Liu, Jie Zhou and Kevin P. White* - Bioinformatics (2014) 30 (3): 301-304. |
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633 |
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634 - http://www.ncbi.nlm.nih.gov/pubmed/24319002 |
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635 - http://dx.doi.org/10.1093/bioinformatics/btt688 |
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636 |
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637 Contact |
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638 ------- |
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639 |
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640 The tool wrapper has been written by Youri Hoogstrate from the Erasmus |
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641 Medical Center (Rotterdam, Netherlands) on behalf of the Translational |
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642 Research IT (TraIT) project: |
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643 |
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644 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch |
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645 |
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646 More tools by the Translational Research IT (TraIT) project can be found |
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647 in the following toolsheds: |
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648 |
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649 http://toolshed.dtls.nl/ |
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650 |
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651 http://toolshed.g2.bx.psu.edu |
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652 |
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653 http://testtoolshed.g2.bx.psu.edu/ |
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654 |
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655 I would like to thank Hina Riaz - Naz Khan for her helpful contribution. |
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656 </help> |
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657 |
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658 <citations> |
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659 <citation type="doi">10.1093/bioinformatics/btp616</citation> |
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660 <citation type="doi">10.1093/bioinformatics/btt688</citation> |
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661 </citations> |
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662 </tool> |