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chore: updateDocumentation
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edkerk committed Sep 27, 2024
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137 changes: 70 additions & 67 deletions doc/INIT/getINITModel.html
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Expand Up @@ -544,77 +544,80 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0391 <span class="keyword">if</span> isfield(model,<span class="string">'geneShortNames'</span>)
0392 model.geneShortNames(I)=[];
0393 <span class="keyword">end</span>
0394 <span class="keyword">if</span> isfield(model,<span class="string">'geneMiriams'</span>)
0395 model.geneMiriams(I)=[];
0394 <span class="keyword">if</span> isfield(model,<span class="string">'proteinNames'</span>)
0395 model.proteinNames(I)=[];
0396 <span class="keyword">end</span>
0397 <span class="keyword">if</span> isfield(model,<span class="string">'geneFrom'</span>)
0398 model.geneFrom(I)=[];
0397 <span class="keyword">if</span> isfield(model,<span class="string">'geneMiriams'</span>)
0398 model.geneMiriams(I)=[];
0399 <span class="keyword">end</span>
0400 <span class="keyword">if</span> isfield(model,<span class="string">'geneComps'</span>)
0401 model.geneComps(I)=[];
0400 <span class="keyword">if</span> isfield(model,<span class="string">'geneFrom'</span>)
0401 model.geneFrom(I)=[];
0402 <span class="keyword">end</span>
0403
0404 <span class="comment">%At this stage the model will contain some exchange reactions but probably</span>
0405 <span class="comment">%not all (and maybe zero). This can be inconvenient, so all exchange</span>
0406 <span class="comment">%reactions from the reference model are added, except for those which</span>
0407 <span class="comment">%involve metabolites that are not in the model.</span>
0408
0409 <span class="comment">%First delete and included exchange reactions in order to prevent the order</span>
0410 <span class="comment">%from changing</span>
0411 model=removeReactions(model,getExchangeRxns(model));
0412
0413 <span class="comment">%Create a model with only the exchange reactions in refModel</span>
0414 excModel=removeReactions(refModel,setdiff(refModel.rxns,getExchangeRxns(refModel)),true,true);
0403 <span class="keyword">if</span> isfield(model,<span class="string">'geneComps'</span>)
0404 model.geneComps(I)=[];
0405 <span class="keyword">end</span>
0406
0407 <span class="comment">%At this stage the model will contain some exchange reactions but probably</span>
0408 <span class="comment">%not all (and maybe zero). This can be inconvenient, so all exchange</span>
0409 <span class="comment">%reactions from the reference model are added, except for those which</span>
0410 <span class="comment">%involve metabolites that are not in the model.</span>
0411
0412 <span class="comment">%First delete and included exchange reactions in order to prevent the order</span>
0413 <span class="comment">%from changing</span>
0414 model=removeReactions(model,getExchangeRxns(model));
0415
0416 <span class="comment">%Find the metabolites there which are not exchange metabolites and which do</span>
0417 <span class="comment">%not exist in the output model</span>
0418 I=~ismember(excModel.mets,model.mets) &amp; excModel.unconstrained==0;
0419
0420 <span class="comment">%Then find those reactions and delete them</span>
0421 [~, J]=find(excModel.S(I,:));
0422 excModel=removeReactions(excModel,J,true,true);
0423
0424 <span class="comment">%Merge with the output model</span>
0425 model=mergeModels({model;excModel},<span class="string">'metNames'</span>);
0426 model.id=<span class="string">'INITModel'</span>;
0427 model.name=[<span class="string">'Automatically generated model for '</span> tissue];
0428 <span class="keyword">if</span> any(celltype)
0429 model.name=[model.name <span class="string">' - '</span> celltype];
0430 <span class="keyword">end</span>
0431
0432 <span class="keyword">if</span> printReport==true
0433 <a href="#_sub1" class="code" title="subfunction [rxnS, geneS]=printScores(model,name,hpaData,arrayData,tissue,celltype)">printScores</a>(model,<span class="string">'Final model statistics'</span>,hpaData,arrayData,tissue,celltype);
0434 <span class="keyword">end</span>
0435
0436 <span class="comment">%Add information about essential reactions and reactions included for</span>
0437 <span class="comment">%gap-filling and return a taskReport</span>
0438 <span class="keyword">if</span> ~isempty(taskStructure)
0439 I=find(taskReport.ok); <span class="comment">%Ignore failed tasks</span>
0440 <span class="keyword">for</span> i=1:numel(I)
0441 taskReport.essential{I(i),1}=cModel.rxns(essentialRxnMat(:,I(i)));
0442 taskReport.gapfill{I(i),1}=refModelNoExc.rxns(addedRxnMat(:,i));
0443 <span class="keyword">end</span>
0444 <span class="keyword">else</span>
0445 taskReport=[];
0446 <span class="keyword">end</span>
0447
0448 <span class="comment">%Fix grRules and reconstruct rxnGeneMat</span>
0449 [grRules,rxnGeneMat] = standardizeGrRules(model,true);
0450 model.grRules = grRules;
0451 model.rxnGeneMat = rxnGeneMat;
0452 <span class="keyword">end</span>
0453
0454 <span class="comment">%This is for printing a summary of a model</span>
0455 <a name="_sub1" href="#_subfunctions" class="code">function [rxnS, geneS]=printScores(model,name,hpaData,arrayData,tissue,celltype)</a>
0456 [a, b]=scoreModel(model,hpaData,arrayData,tissue,celltype);
0457 rxnS=mean(a);
0458 geneS=mean(b(~isinf(b)));
0459 fprintf([name <span class="string">':\n'</span>]);
0460 fprintf([<span class="string">'\t'</span> num2str(numel(model.rxns)) <span class="string">' reactions, '</span> num2str(numel(model.genes)) <span class="string">' genes\n'</span>]);
0461 fprintf([<span class="string">'\tMean reaction score: '</span> num2str(rxnS) <span class="string">'\n'</span>]);
0462 fprintf([<span class="string">'\tMean gene score: '</span> num2str(geneS) <span class="string">'\n'</span>]);
0463 fprintf([<span class="string">'\tReactions with positive scores: '</span> num2str(100*sum(a&gt;0)/numel(a)) <span class="string">'%%\n\n'</span>]);
0464 <span class="keyword">end</span></pre></div>
0416 <span class="comment">%Create a model with only the exchange reactions in refModel</span>
0417 excModel=removeReactions(refModel,setdiff(refModel.rxns,getExchangeRxns(refModel)),true,true);
0418
0419 <span class="comment">%Find the metabolites there which are not exchange metabolites and which do</span>
0420 <span class="comment">%not exist in the output model</span>
0421 I=~ismember(excModel.mets,model.mets) &amp; excModel.unconstrained==0;
0422
0423 <span class="comment">%Then find those reactions and delete them</span>
0424 [~, J]=find(excModel.S(I,:));
0425 excModel=removeReactions(excModel,J,true,true);
0426
0427 <span class="comment">%Merge with the output model</span>
0428 model=mergeModels({model;excModel},<span class="string">'metNames'</span>);
0429 model.id=<span class="string">'INITModel'</span>;
0430 model.name=[<span class="string">'Automatically generated model for '</span> tissue];
0431 <span class="keyword">if</span> any(celltype)
0432 model.name=[model.name <span class="string">' - '</span> celltype];
0433 <span class="keyword">end</span>
0434
0435 <span class="keyword">if</span> printReport==true
0436 <a href="#_sub1" class="code" title="subfunction [rxnS, geneS]=printScores(model,name,hpaData,arrayData,tissue,celltype)">printScores</a>(model,<span class="string">'Final model statistics'</span>,hpaData,arrayData,tissue,celltype);
0437 <span class="keyword">end</span>
0438
0439 <span class="comment">%Add information about essential reactions and reactions included for</span>
0440 <span class="comment">%gap-filling and return a taskReport</span>
0441 <span class="keyword">if</span> ~isempty(taskStructure)
0442 I=find(taskReport.ok); <span class="comment">%Ignore failed tasks</span>
0443 <span class="keyword">for</span> i=1:numel(I)
0444 taskReport.essential{I(i),1}=cModel.rxns(essentialRxnMat(:,I(i)));
0445 taskReport.gapfill{I(i),1}=refModelNoExc.rxns(addedRxnMat(:,i));
0446 <span class="keyword">end</span>
0447 <span class="keyword">else</span>
0448 taskReport=[];
0449 <span class="keyword">end</span>
0450
0451 <span class="comment">%Fix grRules and reconstruct rxnGeneMat</span>
0452 [grRules,rxnGeneMat] = standardizeGrRules(model,true);
0453 model.grRules = grRules;
0454 model.rxnGeneMat = rxnGeneMat;
0455 <span class="keyword">end</span>
0456
0457 <span class="comment">%This is for printing a summary of a model</span>
0458 <a name="_sub1" href="#_subfunctions" class="code">function [rxnS, geneS]=printScores(model,name,hpaData,arrayData,tissue,celltype)</a>
0459 [a, b]=scoreModel(model,hpaData,arrayData,tissue,celltype);
0460 rxnS=mean(a);
0461 geneS=mean(b(~isinf(b)));
0462 fprintf([name <span class="string">':\n'</span>]);
0463 fprintf([<span class="string">'\t'</span> num2str(numel(model.rxns)) <span class="string">' reactions, '</span> num2str(numel(model.genes)) <span class="string">' genes\n'</span>]);
0464 fprintf([<span class="string">'\tMean reaction score: '</span> num2str(rxnS) <span class="string">'\n'</span>]);
0465 fprintf([<span class="string">'\tMean gene score: '</span> num2str(geneS) <span class="string">'\n'</span>]);
0466 fprintf([<span class="string">'\tReactions with positive scores: '</span> num2str(100*sum(a&gt;0)/numel(a)) <span class="string">'%%\n\n'</span>]);
0467 <span class="keyword">end</span></pre></div>
<hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
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