Extend a Parameter Values Building Block (BB) with protein expression parameters for selected protein molecules in selected organs.

For each protein in moleculeNames, parameters defining the protein expression (e.g. "Relative expression", "Fraction expressed ...", and "Initial concentration" entries) are added to the parameterValuesBuildingBlock for every physical container under each path in organPaths. Default values are taken from the reference expression profile supplied for that molecule. Existing entries are not overwritten.

Usage

addProteinExpressionToParameterValuesBB(
  parameterValuesBuildingBlock,
  spatialStructureModule,
  moleculesModule,
  moleculeNames = NULL,
  referenceExpressionProfiles = NULL,
  organPaths = NULL
)

Arguments

parameterValuesBuildingBlock

A BuildingBlock object of type Parameter Values. The entries will be added to this building block.

spatialStructureModule

A MoBiModule containing a Spatial Structure building block. Expression parameters are created for containers defined by this spatial structure.

moleculesModule

A MoBiModule containing a Molecules building block. Must contain the proteins named in moleculeNames.

moleculeNames

Character vector of protein molecule names for which expression parameters should be added. If NULL (default), all proteins (i.e. molecules of type Enzyme, Transporter, or Binding Partner) defined in the Molecules building block of moleculesModule are used.

referenceExpressionProfiles

A single BuildingBlock of type Expression Profile, a list of such building blocks, or NULL. The matching profile for each molecule in moleculeNames is identified by the profile's MoleculeName property. For every molecule in moleculeNames without a supplied profile (or when this argument is NULL), a default profile is created via createExpressionProfileBuildingBlock() for species "Human", using the molecule's protein type to choose the profile category (Enzyme -> Metabolizing Enzyme, Transporter -> Transport Protein, Binding Partner -> Protein Binding Partner). Profiles whose MoleculeName is not in moleculeNames are ignored. Duplicate profiles (two entries with the same MoleculeName) raise an error.

organPaths

Character vector of organ paths under which expression parameters are created (e.g. "Organism|Kidney"). Each path must resolve to an existing organ in the spatial structure. The parameters are added for all physical containers under these paths. If NULL (default), expression parameters are created for every organ in the spatial structure.

Value

Paths of entries added to the building block.

Examples

if (FALSE) { # \dontrun{
project <- loadMoBiProject("path/to/project.mbp3")
module <- project$getModules("TestModule")[[1]]
pvBB <- module$getParameterValuesBBs()[[1]]
profile <- project$getExpressionProfiles("CYP3A4|Human|Healthy")[[1]]

# Use a supplied reference profile and target one organ.
newPaths <- addProteinExpressionToParameterValuesBB(
  parameterValuesBuildingBlock = pvBB,
  spatialStructureModule = module,
  moleculesModule = module,
  moleculeNames = "CYP3A4",
  referenceExpressionProfiles = profile,
  organPaths = "Organism|Kidney"
)

# Auto-resolve protein names from the Molecules BB and create default
# `Human` profiles for any molecule without a supplied reference profile.
newPaths <- addProteinExpressionToParameterValuesBB(
  parameterValuesBuildingBlock = pvBB,
  spatialStructureModule = module,
  moleculesModule = module
)
} # }