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Change renamed similar function in tutorial
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NicolasSompairac committed Dec 8, 2017
1 parent c92697d commit 6300023
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Expand Up @@ -446,35 +446,37 @@
%% *2. Research of indexes in the map structure*
% Basic functions were created to simplify the manipulation of maps.
%
% The function |findRxnsPerType| gives a list of desired reactions based
% The function |findRxnsPerTypeInMap| gives a list of desired reactions based
% on the reaction type (2nd colum), and the index for those reactions in |map.rxnName|
% (1st colum).
%%
transportReactionsIndexList = findRxnsPerType(mapGlyCorrected, 'TRANSPORT');
transportReactionsIndexList = findRxnsPerTypeInMap(mapGlyCorrected, 'TRANSPORT');
%%
% The function |findMetsIDs| finds the IDs of specific metabolites in |map.specName|
% given a list of metabolites.
% The function |findMetsInMap| finds the IDs of specific metabolites in
% |map.specName| given a list of metabolites.

ATPADPIndexList = findMetsIDs(mapGlyCorrected, ...
ATPADPIndexList = findMetsInMap(mapGlyCorrected, ...
{'atp[c]', 'adp[c]', 'atp[m]', 'adp[m]'});
%%
% The function |findRxnsIDs| finds the IDs of specific reactions in |map.rxnName|
% The function |findRxnsInMap| finds the IDs of specific reactions in |map.rxnName|
% given a list of reactions.

rxnOfInterestIndexList = findRxnsIDs(mapGlyCorrected, ...
rxnOfInterestIndexList = findRxnsInMap(mapGlyCorrected, ...
{'FBP', 'FBA', 'GAPD', 'PFK', 'ENO'});
%%
% The function |findMetFromCompartMap| finds all metabolites in the map
% The function |findMetsFromCompartInMap| finds all metabolites in the map
% associated to a specific compartment by looking at the composition of metabolite
% names (example: mitochondrial atp = atp*[m]*).

[mitochondrialMetsNameList,mitochondrialMetsIndexList] = ...
findMetFromCompartMap(mapGlyCorrected, '[m]');
findMetsFromCompartInMap(mapGlyCorrected, '[m]');
%%
% The function |findRxnFromCompartMap| finds all reactions in the map associated
% to a specific compartment by looking at the composition of metabolite names.
% The function |findRxnsFromCompartInMap| finds all reactions in the map
% associated to a specific compartment by looking at the composition of metabolite
% names.

mitochondrialRxnsIndexList = findRxnFromCompartMap(mapGlyCorrected, '[m]');
mitochondrialRxnsIndexList = ...
findRxnsFromCompartInMap(mapGlyCorrected, '[m]');
%% Visualisation of Metabolic and PPI networks
% Some of the aforementioned functions were addapted to be used in metabolic
% and PPi maps. Some examples are shown below:
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