The invitroTKstats
R package contains functions to run a
standardized data pipeline for processing high-throughput toxicokinetic
(HTTK) mass-spectrometry data obtained from a variety of in
vitro assays. The pipeline includes standardization for data
documentation, statistical analyses predicting toxicokinetic parameters
characterizing absorption, distribution, metabolism, and elimination of
chemicals by the body.
The assays covered by the pipeline include intrinsic clearance after hepatocyte incubation (\(Cl_{int}\)); two variants of plasma protein binding experiments (\(f_{up}\)) – namely Rapid Equilibrium Dialysis (RED) and Ultracentrifugation (UC), CACO-2 membrane permeability, and blood to plasma concentration ratio. Analysis methods include a frequentist point estimation and, in some cases, Bayesian estimations for the distribution of likely parameter values. Data used to derive the estimates are based on mass spectrometry ratios of analyte peak areas to internal standard (ISTD) peak areas.
If you are interested in contributing or want to report a bug, please submit an issue or start a discussion.
Additional background information on dosimetry and use of these estimates may be found here.
invitroTKstats
:
ggplot2
parallel
runjags
stats4
::install_github("https://github.com/USEPA/invitroTKstats") devtools
Installing a local clone of the GitHub repo:
invitroTKstats
.git clone https://github.com/USEPA/invitroTKstats
.::install_local(
devtools"<file_path_to_invitroTKstats_repo>/invitroTKstats"
)
Installing a tarball version of the package:
R CMD INSTALL <file_path_to_invitroTKstats_tarball>/invitroTKstats_X.Y.Z.tar.gz
NOTE: “X.Y.Z” in the tarball filename indicates the version number associated with the version of the package you wish to install.
To load the invitroTKstats
R package into your local R
session via the R console:
library(invitroTKstats)
Check the package version installed and in use:
packageVersion(invitroTKstats)
A subset of raw experimental data files are provided as part of the R package for demonstration purposes in the “Data Guide Creation and Level-0 Data Compilation” vignette. These data files were originally published as part of Kreutz et al. (2023). Details about these files can be found in the README file under the “inst/extdata/Kreutz-Clint” sub-directory, as well as a separate data processing GitHub repository invitrotkstats_dataproc under “working/KreutzPFAS”.
The United States Environmental Protection Agency (EPA) GitHub project code is provided on an “as is” basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity, confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.