shrinkMatrix-methods: Get a Subset of Matrix Like Objects

In SysBioChalmers/sybil: Efficient Constrained Based Modelling

Get a Subset of Matrix Like Objects

Description

Generate subsets of matrix-like objects.

Usage

## S4 method for signature 'modelorg'
shrinkMatrix(X, i = NULL, j = NULL,
                                  tol = SYBIL_SETTINGS("TOLERANCE"))

Arguments

X	An object treated to be matrix-like.
i	A numeric or character vector containing row indices of the matrix given in argument X. For the modelorg method, this can be an object of class reactId_Exch. Default: NULL.
j	A numeric or character vector containing column indices of the matrix given in argument X. For the modelorg method, this can be an object of class reactId. Default: NULL.
tol	A tolerance value. An element X_{ij} of the matrix given in argument X is considered to be zero, if |X_{ij}| > \mathit{tol} is true. Default: SYBIL_SETTINGS("TOLERANCE").

Value

The modelorg method will return an object of class Matrix, with columns named by their reaction id's and rows named by their metabolite id's.

Methods

signature(X = "modelorg")

method to use with objects of class modelorg for subsets of the stoichiometric matrix. Either argument i or argument j can be used, not both at the same time. If they are of type character, they must contain metabolite or reaction id's existing in the modelorg object. Use i to get the reactions in which the metabolites given in i participate (the metabolites given in i will be located in the first rows of the result). Use j to get all reactions given in j. The method will remove all non-zero rows and columns from the result.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

Class modelorg.

Examples

  # get the part of the stoichiometric containing
  # the exchange reactions
  data(Ec_core)
  ex <- findExchReact(Ec_core)
  shrinkMatrix(Ec_core, j = ex)

SysBioChalmers/sybil documentation built on Aug. 24, 2023, 1:08 p.m.