multiDel: Parallel Support for sybil

In SysBioChalmers/sybil: Efficient Constrained Based Modelling

Parallel Support for sybil

Description

Parallel computation support for the functions oneGeneDel, doubleGeneDel, oneFluxDel, doubleFluxDel and fluxVar.

Usage

  multiDel(model, nProc = 2, todo = "oneGeneDel", del1 = NA, del2 = NA, ...)

Arguments

model	An object of class modelorg.
nProc	Number of cores (processes) to use.
todo	A single character value giving the function name, which should be parallelised. Can be one of "oneGeneDel", "doubleGeneDel", "oneFluxDel", "doubleFluxDel" or "fluxVar".
del1	Vector of genes/reactions to consider.
del2	Vector of genes/reactions to consider (for use with doubleGeneDel or doubleFluxDel).
...	Further arguments passed to oneGeneDel, doubleGeneDel, oneFluxDel, doubleFluxDel or fluxVar.

Details

The function loads the package parallel if available. Argument nProc should be the number of cores to use. This number is veryfied via a call to detectCores (of parallel) and is set to the return value of detectCores, if nProc > detectCores() evaluates to TRUE. Arguments del1 and del2 are split into lists, each list element containing nProc/del1 elements. These are passed to mclapply.

Value

A list of length nProc (or less, depending of the numbers of available cores), each element containing the return value of the function called (on object of a class extending optsol).

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

mclapply, optsol, oneGeneDel, doubleGeneDel, oneFluxDel, doubleFluxDel and fluxVar.

Examples

## Not run: 
## The examples here require the packages glpkAPI and parallel to be
## installed.

## perform single gene deletion analysis using the E. coli core
## metabolic model
data(Ec_core)
ad <- multiDel(Ec_core)
mapply(checkOptSol, ad)

## End(Not run)

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