ROOM implementation (Regulatory on/off minimization of metabolic flux changes) #1425
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tpfau
reviewed
Feb 13, 2019
src/analysis/ROOM/ROOM.m
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| addRequired(p, 'WTflux', @(x)isnumeric(x)&&isvector(x)); | ||
| addRequired(p, 'rxnKO', @(x)iscell(x)); | ||
| % Check optional arguments | ||
| addOptional(p, 'delta', 0.03, @(x)isnumeric(x)&&isscalar(x)); |
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is it intentional, that these are positioned optional arguments instead of parameters?
The same applies to the linearROOM version.
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Thanks @tpfau for the comment. When I first wrote the code I considered they were more used a, as they are part of the mathematical model. I will change them to paramenters.
Codecov Report
@@ Coverage Diff @@
## develop #1425 +/- ##
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+ Coverage 44.42% 44.43% +0.01%
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Files 902 904 +2
Lines 64592 64679 +87
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+ Hits 28693 28740 +47
- Misses 35899 35939 +40
Continue to review full report at Codecov.
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Thanks @lvalcarcel and @tpfau 👍 |
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Implementation of ROOM (Regulatory on/off minimization of metabolic flux changes) using COBRA functionalities.
Shlomi, Tomer, Omer Berkman, and Eytan Ruppin. "Regulatory on/off minimization of metabolic flux changes after genetic perturbations." Proceedings of the National Academy of Sciences 102.21 (2005): 7695-7700.
The main article can be found in: https://www.pnas.org/content/102/21/7695.short
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