sybil: multiDel – R documentation

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multiDel

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 <geliudie@uni-duesseldorf.de>

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

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)

sybil

Efficient Constrained Based Modelling

v2.1.5

GPL-3 | file LICENSE

Authors

Mayo Roettger [cre], Gabriel Gelius-Dietrich [aut], C. Jonathan Fritzemeier [ctb], Rajen Piernikarczyk [ctb], Marc Andre Daxer [ctb], Benjamin Braasch [ctb], Abdelmoneim Desouki [ctb], Martin J. Lercher [ctb]

Initial release

2019-03-07