Create a new expression profile — create_expression

Create an ExpressionProfile building block from named arguments. This is a thin factory around ExpressionProfile$new() that builds the raw list shape for you.

An ExpressionProfile's identity is the composite Molecule|Species|Category, so all three of molecule, species, and category are required.

Usage

create_expression_profile(
  molecule,
  species,
  category,
  type,
  localization = NULL,
  transport_type = NULL,
  ontogeny = NULL,
  parameters = NULL,
  expression = NULL,
  disease = NULL,
  description = NULL
)

Arguments

molecule: Character. Name of the molecule (for example "CYP3A4"). Required.
species: Character. Species (for example "Human"). Required.
category: Character. Category disambiguator (for example "Healthy" or "Variability"). Required.
type: Character. Molecule type, typically one of "Enzyme", "Transporter", or "OtherProtein". Required.
localization: Character. Expression localization for proteins.
transport_type: Character. Transporter type (for transporter profiles), for example "Efflux" or "Influx".
ontogeny: Character or list. Ontogeny name, or a raw ontogeny list. If a string is supplied it is wrapped as list(Name = ontogeny).
parameters: List of Parameter objects (created with create_parameter()) or raw parameter lists describing relative expression and other per-organ values.
expression: Per-organ relative expression, written to the snapshot's Expression array. Supply a data frame (or tibble), one row per organ/compartment, with a required name column (organ/container name, for example "Liver") and the optional columns value (relative expression), compartment (for example "Intracellular"), and transport_direction (for transporter profiles). Missing (NA) or absent optional cells emit no key, so a row with only name and value produces a container with just those two fields. Row order is preserved and duplicate names are kept. Alternatively supply a raw list of container lists (each a named list with any of Name, Value, CompartmentName, TransportDirection) to pass through verbatim. NULL or an empty input writes nothing.
disease: Disease state, written to the snapshot's Disease object. Supply a named list with name (required, the DiseaseState name) and an optional parameters list of Parameter objects or raw parameter lists. NULL writes nothing.
description: Character. Free-text description of the profile.

Value

An ExpressionProfile object.

Examples

# Create a minimal enzyme expression profile
profile <- create_expression_profile(
  molecule = "CYP3A4",
  species = "Human",
  category = "Healthy",
  type = "Enzyme"
)

# Create a transporter expression profile with ontogeny
profile <- create_expression_profile(
  molecule = "P-gp",
  species = "Human",
  category = "Healthy",
  type = "Transporter",
  transport_type = "Efflux",
  ontogeny = "P-gp"
)

# Create an enzyme profile with per-organ relative expression
profile <- create_expression_profile(
  molecule = "CYP3A4",
  species = "Human",
  category = "Healthy",
  type = "Enzyme",
  expression = data.frame(
    name = c("Liver", "Kidney"),
    value = c(1, 0.5)
  )
)