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comparison COBRAxy/flux_to_map.xml @ 19:505b8574c017 draft

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author luca_milaz
date Wed, 18 Sep 2024 12:49:47 +0000
parents 41f35c2f0c7b
children 10e8386ed410
comparison
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18:e962ba5fc27d 19:505b8574c017
152 152
153 Optional files: 153 Optional files:
154 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example. 154 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
155 155
156 The tool generates: 156 The tool generates:
157 - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes; 157 - 1) a tab-separated file: reporting fold-change and p-values of fluxes between a pair of conditions/classes;
158 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes; 158 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
159 - 3) a log file (.txt). 159 - 3) a log file (.txt).
160 160
161 Output options: 161 Output options:
162 To calculate P-Values and Fold-Changes and to enrich maps, comparisons are performed for each possible pair of groups (default option ‘One vs One’). 162 To calculate P-Values and Fold-Changes and to enrich maps, comparisons are performed for each possible pair of groups (default option ‘One vs One’).
168 Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA". 168 Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA".
169 169
170 Example input 170 Example input
171 ------------- 171 -------------
172 172
173 "RAS of group 1 + RAS of group 2 + ... + RAS of group N" option: 173 "Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N" option:
174 174
175 RAS Dataset 1: 175 Fluxes Dataset 1:
176 176
177 +------------+----------------+----------------+----------------+ 177 +------------+----------------+----------------+----------------+
178 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 | 178 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
179 +============+================+================+================+ 179 +============+================+================+================+
180 | r1642 | 0.523167 | 0.371355 | 0.925661 | 180 | r1642 | 0.523167 | 0.371355 | 0.925661 |
186 | r1641 | 0.456788 | 0.876543 | 0.876542 | 186 | r1641 | 0.456788 | 0.876543 | 0.876542 |
187 +------------+----------------+----------------+----------------+ 187 +------------+----------------+----------------+----------------+
188 | r1646 | 0.876543 | 0.786543 | 0.897654 | 188 | r1646 | 0.876543 | 0.786543 | 0.897654 |
189 +------------+----------------+----------------+----------------+ 189 +------------+----------------+----------------+----------------+
190 190
191 RAS Dataset 2: 191 Fluxes Dataset 2:
192 192
193 +------------+----------------+----------------+----------------+ 193 +------------+----------------+----------------+----------------+
194 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 | 194 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
195 +============+================+================+================+ 195 +============+================+================+================+
196 | r1642 | 0.523167 | 0.371355 | 0.925661 | 196 | r1642 | 0.523167 | 0.371355 | 0.925661 |
202 | r1641 | 0.456788 | 0.876543 | 0.876542 | 202 | r1641 | 0.456788 | 0.876543 | 0.876542 |
203 +------------+----------------+----------------+----------------+ 203 +------------+----------------+----------------+----------------+
204 | r1646 | 0.876543 | 0.786543 | 0.897654 | 204 | r1646 | 0.876543 | 0.786543 | 0.897654 |
205 +------------+----------------+----------------+----------------+ 205 +------------+----------------+----------------+----------------+
206 206
207 "RAS of all samples + sample group specification" option: 207 "Fluxes of all samples + sample group specification" option:
208 208
209 RAS Dataset: 209 Fluxes Dataset:
210 210
211 +------------+----------------+----------------+----------------+ 211 +------------+----------------+----------------+----------------+
212 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 | 212 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
213 +============+================+================+================+ 213 +============+================+================+================+
214 | r1642 | 0.523167 | 0.371355 | 0.925661 | 214 | r1642 | 0.523167 | 0.371355 | 0.925661 |
237 237
238 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_. 238 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
239 239
240 .. class:: infomark 240 .. class:: infomark
241 241
242 **TIP**: This tool using the RAS scores computed by `Ras tool`_.
243 242
244 ]]> 243 ]]>
245 </help> 244 </help>
246 <expand macro="citations" /> 245 <expand macro="citations" />
247 </tool> 246 </tool>