emba (version 0.1.1)

get_link_operators_from_models_dir: Load the models boolean equation link operator data

Description

Use this function to merge the link operator data used in the boolean equations of the models into a single matrix. Every boolean model is defined by a series of boolean equations in the form \(Target *= (Activator OR Activator OR...) AND NOT (Inhibitor OR Inhibitor OR...)"\). The link operator can be either AND NOT, OR NOT or non-existent if the target has only activating regulators or only inhibiting ones. The models are loaded from .gitsbe files that can be found inside the given models.dir directory.

Usage

get_link_operators_from_models_dir(models.dir,
  remove.equations.without.link.operator = TRUE)

Arguments

models.dir

string. A dir with .gitsbe files/models

remove.equations.without.link.operator

logical. Should we keep the nodes (columns in the returned matrix) which do not have both type of regulators (so no link operator)? Default value: TRUE (remove these nodes).

Value

a matrix (nxm) with n models and m nodes. The row names of the matrix specify the models' names whereas the column names specify the name of the network nodes (gene, proteins, etc.). Possible values for each model-node element are either 0 (AND NOT link operator), 1 (OR NOT link operator) or 0.5 if the node is not targeted by both activating and inhibiting regulators (no link operator).

Examples

# NOT RUN {
models.dir = system.file("extdata", "models", package = "emba", mustWork = TRUE)
models.link.operator = get_link_operators_from_models_dir(models.dir)
models.link.operator.with.extra.nodes =
  get_link_operators_from_models_dir(models.dir, FALSE)

# }