R/input.R
get_link_operators_from_models_dir.Rd
Use this function to merge the link operator data used in the boolean equations
of the models into a single data.frame
object. 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 not remains in the
latter case). The models are loaded from .gitsbe files (and only these)
that can be found inside the given models.dir
directory.
get_link_operators_from_models_dir( models.dir, remove.equations.without.link.operator = TRUE )
models.dir | string. A directory path with .gitsbe files/models. Do not include the ending path character in the string (/). |
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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). |
a data.frame
(nxm) with n models and m nodes. The row names
specify the models' names whereas the column names specify 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).
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)