Description Usage Arguments Value Examples

View source: R/minimal_perturbation.R

Assemble the LP problem for minimal perturbation.

1 2 | ```
minimal_perturbation_lp(ma_terms, samples, S, v_min = 0, v_max = 1000,
min_obj = 100)
``` |

`ma_terms` |
A matrix or data frame containing the metabolic terms in the columns. |

`samples` |
A factor or character string with either "normal" and "disease" entries. |

`S` |
The stoichiometric matrix or a list containing one matrix for each sample. |

`v_min` |
The lower bounds for the fluxes. Either a single value for the min bounds for all reactions or a matrix/data.frame with two columns and as many rows as irreversible reactions where the columns contain the lower bounds for each factor level in 'samples'. |

`v_max` |
The upper bounds for the fluxes. Either a single value for the max bounds for all reactions or a matrix/data.frame with two columns and as many rows as irreversible reactions where the columns contain the upper bounds for each factor level in 'samples'. |

`min_obj` |
Constraints for growth rate. If a vector with two elements the first will be interpreted as the index of the objective reaction and the second value as its lower bound. If only a single value will constrain the absolute sum of fluxes (sum |v_i|) and take the value as the lower bound. |

A list with the following components:

- coefficients
The coefficients for the equalities/inequalities in the LP. Each row denotes one equation.

- type
The type of the (in)equalities. A character vector with as many entries as rows in 'coefficients' being either "equal", "less" or "larger"

- bounds
A matrix with two columns containing the upper and lower variable (flux) bounds.

- row_bounds
Vector containing the right sides to the (in)equalities.

- obj_coefs
The objective coefficients. Containing one number for each variable.

1 |

cdiener/dycone documentation built on Sept. 9, 2018, 1:20 p.m.

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