sybil (version 1.0.2)

geneDeletion: Simulate N Gene Deletion Experiments

Description

The function geneDeletion studies the effect of in sillico gene deletions on the current objective function (e.g. biomass production).

Usage

geneDeletion(model, genes, combinations = 1,
               lpdir = SYBIL_SETTINGS("OPT_DIRECTION"),
               solver = SYBIL_SETTINGS("SOLVER"),
               method = SYBIL_SETTINGS("METHOD"),
               fld = FALSE, ...)

Arguments

model

An object of class modelorg.

genes

Character or Integer: the genes to delete (see Details below).

combinations

A single integer value. If combinations > 1 and genes is not a matrix, combinations is the number of elements from genes taken at a time while building all combinations of the elements in

lpdir

Character value, direction of optimisation. Can be set to "min" or "max". Default: SYBIL_SETTINGS("OPT_DIRECTION").

solver

Single character value. The solver to use. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTINGS("SOLVER").

method

Single character value. The optimization algorithm to use. Possible values depend on the setting in solver. See SYBIL_SETTINGS for possible values. Default: SYBIL_SETTIN

fld

Boolean. Save the resulting flux distribution. Default: FALSE.

...

Further arguments passed to optimizer.

Value

• An object of class optsol_genedel. Its first element will allways be a wild type solution, with no gene deleted.

encoding

utf8

Details

If argument genes is a matrix of character values (gene id's) or integers (pointers to gene id's), each column is treated as one deletion experiment. If the matrix is made up of integers, a zero entry means no gene. If argument genes is a character vector or integer, the argument combinations gives the number of gene id's taken each time in order to build all possible combinations of genes. A matrix is constructed using combn. If argument genes is empty, the number of unique genes in model is used.

See Also

modelorg, optsol, optsol_genedel, checkOptSol, oneGeneDel, doubleGeneDel, optimizer, simpleFBA, combn and SYBIL_SETTINGS.

Examples

## load the dataset
  data(Ec_core)
  
  ## perform a single gene deletion analysis (delete every gene one time)
  gd <- geneDeletion(Ec_core)
  
  ## triple gene deletion analysis using the first ten genes
  gd <- geneDeletion(Ec_core, genes = 10, combinations = 3)

## perform a double gene deletion analysis (delete all possible pairwise
  ## combinations of all genes)
  gd <- geneDeletion(Ec_core, combinations = 2)

  ## perform a triple gene deletion analysis
  ## (very high number of optimizations)
  gd <- geneDeletion(Ec_core, combinations = 3)