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

get_invitroPK_param {httk}

R 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