perturbNetworkFixedNodes: Perturb network functions knock-out (0) or over-expression...

In mar-esther23/boolnet-perturb: Perturb Boolean Networks

Description

Simulates fixed function perturbations (knock-out and over-expression) in a network. Takes a network, a list of gene names and corresponding values to perturb, fixes those values in each network and returns the corresponding attractors for all perturbed networks. By default it returns all the single node knock-out and over-expression of a network.

Usage

perturbNetworkFixedNodes(net, genes, values = 0, names,
  returnDataFrame = c("occurrence", "basinSize", "attrList"),
  label.rules = NULL, sep = "/", verbose = FALSE, ...)

Arguments

net	network to perturb
genes	list of gene names to perturb. To perturb multiple nodes at the same time use a vector inside the list.
values	list of values of the perturbed genes. Knock-out is 0, over-expression is 1.
names	names of the perturbation
returnDataFrame	if returnDataFrame='occurrence' returns a df where each column corresponds to a network and the rows to the attractor/label or labels. The values indicate the frequency of the attractor/label if returnDataFrame='basinSize' returns a df where the values indicate the basin size of the attractor/label if returnDataFrame='attrList' returns a list of AttractorInfo objects
label.rules	if label.rules=NULL (default) returns a df with the attractors as rows if label.rules is a dataframe with labels (1st col) and rules (2nd col), if more than one rule is true all labels are appendedl the node names present in the rules must be in node.names
sep	string to join states in cyclic attractors, default "/"
verbose	report the node being perturbed, useful for larger networks
...	Further parameters to getAttractors.

Value

dataframe or list of attractors of the perturbed networks

See Also

fixGenes attractorListToDataframe

Examples

data(cellcycle)
# All single gene knock-out and over-expression of cellcycle network
perturbNetworkFixedNodes(cellcycle)

# Cellcycle network CycD over-expression
perturbNetworkFixedNodes( cellcycle, list("CycD"), list(1) )

# Cellcycle network CycD knock-out with Rb over-expression
perturbNetworkFixedNodes(  cellcycle, list(c("CycD", "Rb")), list(c(0,1)) , list("CycD-RB+") )

# All CycD double gene knock-outs
double.KO <- lapply(cellcycle$genes[-1], function(gene) c("CycD", gene))
number.double.KO <- length(double.KO)
perturbNetworkFixedNodes(  net=cellcycle, genes=double.KO, 
                        value=as.list(rep(0, number.double.KO))  ) 

mar-esther23/boolnet-perturb documentation built on April 21, 2020, 9:11 a.m.