getINITSteps
Converts a reaction score to the gene expression (CPM or TPM) required
to get that reaction score, if the GPR is only a single gene.
Useful function primarily in test cases, where you want to be able to
define the reaction scores of rxns, but need to send in gene expression.
Note that all combinations of steps will not work. In general, avoid 'exclude'
if you want to define new ways to run the algorithm.
metsToIgnore Structure describing mets that can be removed from the model
before running ftINIT, such as water etc.
(optional, default [])
simpleMets
mets Names of metabolites to remove
compsToKeep Compartments for which metabolites should be kept.
series Describes the way to run ftINIT:
'1+1' Standard behavior. Step 1 and 2 described in
the paper are merged into 1.
'2+1' The 3-step procedure described in the paper.
Faster and slightly less accurate than '1+1 steps'
'1+0' Same as '1+1 steps', but skips step 3 in described
in the paper. This will result in a model including
a lot of reactions without GPRs. It is particularly
useful for structural comparison, since the reactions
removed in step 3 may be a bit random and doesn't
really add any extra information. Faster than
'1+1 steps'
'2+0' Same as '2+1 steps', but skips step 3 in described
in the paper. Faster and slightly less accurate
than '1+0 steps', but will yield similar results.
'full' 1-step run - similar to the old tINIT version but
without simplifications. Accurate, but very slow.
This is mainly used for testing purposes.
(optional, default '1+1')
steps Cell array of steps, used as input to ftINIT
Usage: steps = getINITSteps(metsToIgnore, series)0001 function steps = getINITSteps(metsToIgnore, series) 0002 % getINITSteps 0003 % Converts a reaction score to the gene expression (CPM or TPM) required 0004 % to get that reaction score, if the GPR is only a single gene. 0005 % Useful function primarily in test cases, where you want to be able to 0006 % define the reaction scores of rxns, but need to send in gene expression. 0007 % Note that all combinations of steps will not work. In general, avoid 'exclude' 0008 % if you want to define new ways to run the algorithm. 0009 % 0010 % metsToIgnore Structure describing mets that can be removed from the model 0011 % before running ftINIT, such as water etc. 0012 % (optional, default []) 0013 % simpleMets 0014 % mets Names of metabolites to remove 0015 % compsToKeep Compartments for which metabolites should be kept. 0016 % series Describes the way to run ftINIT: 0017 % '1+1' Standard behavior. Step 1 and 2 described in 0018 % the paper are merged into 1. 0019 % '2+1' The 3-step procedure described in the paper. 0020 % Faster and slightly less accurate than '1+1 steps' 0021 % '1+0' Same as '1+1 steps', but skips step 3 in described 0022 % in the paper. This will result in a model including 0023 % a lot of reactions without GPRs. It is particularly 0024 % useful for structural comparison, since the reactions 0025 % removed in step 3 may be a bit random and doesn't 0026 % really add any extra information. Faster than 0027 % '1+1 steps' 0028 % '2+0' Same as '2+1 steps', but skips step 3 in described 0029 % in the paper. Faster and slightly less accurate 0030 % than '1+0 steps', but will yield similar results. 0031 % 'full' 1-step run - similar to the old tINIT version but 0032 % without simplifications. Accurate, but very slow. 0033 % This is mainly used for testing purposes. 0034 % (optional, default '1+1') 0035 % 0036 % steps Cell array of steps, used as input to ftINIT 0037 % 0038 % Usage: steps = getINITSteps(metsToIgnore, series) 0039 if nargin < 1 0040 metsToIgnore = []; 0041 end 0042 0043 if nargin < 2 0044 series = '1+1'; 0045 end 0046 0047 if strcmp(series,'1+1') %step 1 and 2 are joined 0048 params1 = struct(); 0049 params1.MIPGap = 0.0004; 0050 params1.TimeLimit = 120; 0051 params2 = struct(); 0052 params2.MIPGap = 0.0030; 0053 params2.TimeLimit = 5000; 0054 params = {params1;params2}; 0055 params3 = struct(); 0056 params3.MIPGap = 0.0004; 0057 params3.TimeLimit = 5; 0058 paramsStep3 = {params3;params1;params2}; 0059 %The paramsStep3 involves a quick first run. The objective value is often 0060 %small in the third step (~800), and 0.0004 of that is a very small number 0061 %With this first step, the rough value of the objective function will be 0062 %estimated, which will generate an absolute MIPGap limit that is much larger 0063 %for the second iteration. 0064 0065 steps = { ... 0066 INITStepDesc(false, false, 'ignore', [1,1,1,1,1,1,1,0], metsToIgnore, params, {10;20}); ... 0067 INITStepDesc(false, false, 'essential', [1,0,0,0,1,0,0,0], metsToIgnore, paramsStep3, {10;10;20}); ... 0068 }; 0069 elseif strcmp(series,'2+1') %the 3 step process described in the ftINIT paper 0070 params1 = struct(); 0071 params1.MIPGap = 0.0004; 0072 params1.TimeLimit = 120; 0073 params2 = struct(); 0074 params2.MIPGap = 0.0030; 0075 params2.TimeLimit = 5000; 0076 params = {params1;params2}; 0077 params3 = struct(); 0078 params3.MIPGap = 0.0004; 0079 params3.TimeLimit = 5; 0080 paramsStep3 = {params3;params1;params2}; 0081 %The paramsStep3 involves a quick first run. The objective value is often 0082 %small in the third step (~800), and 0.0004 of that is a very small number 0083 %With this first step, the rough value of the objective function will be 0084 %estimated, which will generate an absolute MIPGap limit that is much larger 0085 %for the second iteration. 0086 0087 steps = { ... 0088 INITStepDesc(true, true, 'ignore', [1,1,1,1,1,1,1,0], metsToIgnore, params, {10;20}); ... 0089 INITStepDesc(false, false, 'essential', [1,1,1,1,1,1,1,0], metsToIgnore, params, {10;20}); ... 0090 INITStepDesc(false, false, 'essential', [1,0,0,0,1,0,0,0], metsToIgnore, paramsStep3, {10;10;20}); ... 0091 }; 0092 elseif strcmp(series,'1+0') %Joins step 1 and 2, skips step 3 0093 params1 = struct(); 0094 params1.MIPGap = 0.0004; 0095 params1.TimeLimit = 120; 0096 params2 = struct(); 0097 params2.MIPGap = 0.0030; 0098 params2.TimeLimit = 5000; 0099 params = {params1;params2}; 0100 steps = { ... 0101 INITStepDesc(false, false, 'ignore', [1,1,1,1,1,1,1,0], metsToIgnore, params, {10;20}); ... 0102 }; 0103 elseif strcmp(series,'2+0') %Skips step 3 0104 params1 = struct(); 0105 params1.MIPGap = 0.0004; 0106 params1.TimeLimit = 120; 0107 params2 = struct(); 0108 params2.MIPGap = 0.0030; 0109 params2.TimeLimit = 5000; 0110 params = {params1;params2}; 0111 steps = { ... 0112 INITStepDesc(true, true, 'ignore', [1,1,1,1,1,1,1,0], metsToIgnore, params, {10;20}); ... 0113 INITStepDesc(false, false, 'essential', [1,1,1,1,1,1,1,0], metsToIgnore, params, {10;20}); ... 0114 }; 0115 elseif strcmp(series,'full') %Just one run, slow on large models, but this is the 'perfect' setup 0116 params1 = struct(); 0117 params1.MIPGap = 0.0004; 0118 params1.TimeLimit = 10000; 0119 params = {params1}; 0120 steps = { ... 0121 INITStepDesc(false, false, 'ignore', [0,0,0,0,0,0,0,0], [], params) ... 0122 }; 0123 else 0124 dispEM(['Invalid series in getINITSteps: ' series]) 0125 end 0126 0127 end