caco2_L0

A subset of tandem mass spectrometry (MS/MS) measurements of Caco-2 assay-specific
data honda2025impactinvitroTKstats. This subset contains samples for 3 test analytes/compounds.

datasets

A set of tools for processing and analyzing in vitro toxicokinetic
measurements in a standardized and reproducible pipeline. The package
was developed to perform frequentist and Bayesian estimation on a
variety of in vitro toxicokinetic measurements including -- but not
limited to -- chemical fraction unbound in the presence of plasma
(f_up), intrinsic hepatic clearance (Clint,
uL/min/million hepatocytes), and membrane permeability for
oral absorption (Caco2). The methods provided
by the package were described in Wambaugh et al. (2019) <doi:10.1093/toxsci/kfz205>.

Caroline Ring

invitroTKstats

In Vitro Toxicokinetic Data Processing and Analysis Pipeline

John Wambaugh

Sarah E. Davidson-Fritz

Lindsay Knupp

Barbara A. Wetmore

Zhao Zhihui

Chantel Nicolas

Anna Kreutz

U.S. Federal Government 

caco2_L0 function

A level-0 data.frame with 48 rows and 17 variables:<dl>
<dt><code>Compound</code></dt>
<dd>Compound name</dd><dt><code>DTXSID</code></dt>
<dd>DSSTox Substance Identifier (CompTox Chemicals Dashboard)</dd><dt><code>Lab.Compound.ID</code></dt>
<dd>Compound ID used in the laboratory</dd><dt><code>Date</code></dt>
<dd>Date MS/MS assay data acquired from instrument</dd><dt><code>Sample</code></dt>
<dd>Sample Name</dd><dt><code>Type</code></dt>
<dd>Type of Caco-2 sample</dd><dt><code>Compound.Conc</code></dt>
<dd>Expected (or nominal) concentration of analyte (for calibration curve)</dd><dt><code>Peak.Area</code></dt>
<dd>Peak area of analyte (target compound)</dd><dt><code>ISTD.Peak.Area</code></dt>
<dd>Peak area of internal standard (pixels)</dd><dt><code>ISTD.Name</code></dt>
<dd>Name of compound used as internal standard (ISTD)</dd><dt><code>Analysis.Params</code></dt>
<dd>General description of chemical analysis method</dd><dt><code>Level0.File</code></dt>
<dd>Name of data file from laboratory that was used to compile level-0 data.frame</dd><dt><code>Level0.Sheet</code></dt>
<dd>Name of "sheet" (for Excel workbooks) from which the laboratory data were read</dd><dt><code>Direction</code></dt>
<dd>Direction of the Caco-2 permeability experiment</dd><dt><code>Vol.Donor</code></dt>
<dd>The media volume (in cm^3) of the donor portion of the Caco-2 experimental well</dd><dt><code>Vol.Receiver</code></dt>
<dd>The media volume (in cm^3) of the receiver portion of the Caco-2 experimental well</dd><dt><code>Dilution.Factor</code></dt>
<dd>Number of times the sample was diluted</dd>
</dl>

Format

Caco-2 Level-0 Example Data set — caco2_L0

A level-0 data.frame with 48 rows and 17 variables:<dl>
<dt><code>Compound</code></dt>
<dd>Compound name</dd>

<dt><code>DTXSID</code></dt>
<dd>DSSTox Substance Identifier (CompTox Chemicals Dashboard)</dd>

<dt><code>Lab.Compound.ID</code></dt>
<dd>Compound ID used in the laboratory</dd>

<dt><code>Date</code></dt>
<dd>Date MS/MS assay data acquired from instrument</dd>

<dt><code>Sample</code></dt>
<dd>Sample Name</dd>

<dt><code>Type</code></dt>
<dd>Type of Caco-2 sample</dd>

<dt><code>Compound.Conc</code></dt>
<dd>Expected (or nominal) concentration of analyte (for calibration curve)</dd>

<dt><code>Peak.Area</code></dt>
<dd>Peak area of analyte (target compound)</dd>

<dt><code>ISTD.Peak.Area</code></dt>
<dd>Peak area of internal standard (pixels)</dd>

<dt><code>ISTD.Name</code></dt>
<dd>Name of compound used as internal standard (ISTD)</dd>

<dt><code>Analysis.Params</code></dt>
<dd>General description of chemical analysis method</dd>

<dt><code>Level0.File</code></dt>
<dd>Name of data file from laboratory that was used to compile level-0 data.frame</dd>

<dt><code>Level0.Sheet</code></dt>
<dd>Name of "sheet" (for Excel workbooks) from which the laboratory data were read</dd>

<dt><code>Direction</code></dt>
<dd>Direction of the Caco-2 permeability experiment</dd>

<dt><code>Vol.Donor</code></dt>
<dd>The media volume (in cm^3) of the donor portion of the Caco-2 experimental well</dd>

<dt><code>Vol.Receiver</code></dt>
<dd>The media volume (in cm^3) of the receiver portion of the Caco-2 experimental well</dd>

<dt><code>Dilution.Factor</code></dt>
<dd>Number of times the sample was diluted</dd>


</dl>

Caco-2 Level-0 Example Data set

caco2_L0: Caco-2 Level-0 Example Data set

Description

Usage

Arguments

Format

References