get_invitroPK_param: Retrieve species-specific in vitro data from...

View source: R/get_invitroPK_param.R

get_invitroPK_paramR Documentation

Retrieve species-specific in vitro data from chem.physical_and_invitro.data table

Description

This function retrieves in vitro PK data (for example, intrinsic metabolic clearance or fraction unbound in plasma) for the the chemical specified by argument "chem.name", "dtxsid", or chem.cas from the table chem.physical_and_invitro.data. This function looks for species-specific values based on the argument "species".

Usage

get_invitroPK_param(
  param,
  species,
  chem.name = NULL,
  chem.cas = NULL,
  dtxsid = NULL
)

Arguments

param

The desired parameters, a vector or single value.

species

Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human").

chem.name

The chemical names that you want parameters for, a vector or single value

chem.cas

The chemical CAS numbers that you want parameters for, a vector or single value

dtxsid

EPA's 'DSSTox Structure ID (https://comptox.epa.gov/dashboard)

Details

Note that this function works with a local version of the chem.physical_and_invitro.data table to allow users to add/modify chemical data (for example, adding new data via add_chemtable or loading in silico predictions distributed with httk via load_sipes2017, load_pradeep2020, load_dawson2021, or load_honda2023).

User can request via argument param (case-insensitive):

Parameter Description Units
[SPECIES].Clint (Primary hepatocyte suspension) intrinsic hepatic clearance. Entries with comma separated values are Bayesian estimates of the Clint distribution - displayed as the median, 95th credible interval (that is quantile 2.5 and 97.5, respectively), and p-value. uL/min/10^6 hepatocytes
[SPECIES].Clint.pValue Probability that there is no clearance observed. Values close to 1 indicate clearance is not statistically significant. none
[SPECIES].Caco2.Pab Caco-2 Apical-to-Basal Membrane Permeability 10^-6 cm/s
[SPECIES].Fabs In vivo measured fraction of an oral dose of chemical absorbed from the gut lumen into the gut unitless fraction
[SPECIES].Fgut In vivo measured fraction of an oral dose of chemical that passes gut metabolism and clearance unitless fraction
[SPECIES].Foral In vivo measued fractional systemic bioavailability of an oral dose, modeled as he product of Fabs * Fgut * Fhep (where Fhep is first pass hepatic metabolism). unitless fraction
[SPECIES].Funbound.plasma Chemical fraction unbound in presence of plasma proteins (fup). Entries with comma separated values are Bayesian estimates of the fup distribution - displayed as the median and 95th credible interval (that is quantile 2.5 and 97.5, respectively). unitless fraction
[SPECIES].Rblood2plasma Chemical concentration blood to plasma ratio unitless ratio

Value

The parameters, either a single value, a named list for a single chemical, or a list of lists

Author(s)

John Wambaugh and Robert Pearce

See Also

chem.physical_and_invitro.data

get_invitroPK_param

add_chemtable


httk documentation built on Sept. 11, 2024, 9:32 p.m.