multiDel: Parallel (Multicore) Support for SyBiL

Description

Multicore 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,

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).

Details

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

Examples

Run this code

## 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)

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