shrinkMatrix-methods: Get a Subset of Matrix Like Objects
In sybil: Efficient Constrained Based Modelling

Description Usage Arguments Value Methods Author(s) See Also Examples

Generate subsets of matrix-like objects.

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

`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[i, j] of the matrix given in argument `X` is considered to be zero, if abs([X[i, j]]) > tol is true. Default: `SYBIL_SETTINGS("TOLERANCE")`.

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.

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.

Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>

Maintainer: Mayo Roettger <mayo.roettger@hhu.de>

Class modelorg.

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