fup_red_PREJAGS: Fup RED Level-4 PREJAGS arguments
In invitroTKstats: In Vitro Toxicokinetic Data Processing and Analysis Pipeline

fup_red_PREJAGS

R Documentation

Fup RED Level-4 PREJAGS arguments

Description

The arguments given to JAGS for the tested compound during level-4 processing of mass spectrometry measurements of plasma protein binding (PPB) via rapid equilibrium dialysis (RED) for per- and poly-fluorinated alkyl substance (PFAS) samples. Experiments were led by Dr.s Marci Smeltz and Barbara Wetmore \insertCitesmeltz2023plasmainvitroTKstats. This list is overwritten for each tested compound. Therefore, only contains arguments given to JAGS for the last tested compound.

Usage

fup_red_PREJAGS

Format

A named list with 33 elements:

Test.Nominal.Conc: Unique Test.Nominal.Conc values (expected initial concentration) for the tested compound
Num.cal: Unique number of Calibration values for the tested compound
Physiological.Protein.Conc: The assumed physiological protein concentration for plasma protein binding calculations. (Defaults to 70/(66.5*1000)*1000000. According to \insertCiteberg2011pathology;textualinvitroTKstats: 60-80 mg/mL, albumin is 66.5 kDa, assume all protein is albumin to estimate default in uM.)
Assay.Protein.Perecent: Percent.Physiologic.Plasma values for each "Plasma" sample type replicate group
Num.Plasma.Blank.obs: Number of "Plasma.Blank" sample types for the tested compound
Plasma.Blank.obs: Response of the "Plasma.Blank" sample types for the tested compound
Plasma.Blank.cal: Indices of the unique Calibration values that corresponds to the "Plasma.Blank" sample types' Calibration for the tested compound
Plasma.Blank.df: Unique Dilution Factor of the "Plasma.Blank" sample types for the tested compound
Plasma.Blank.rep: Integer representing "Plasma.Blank" replicate group for the tested compound
Num.NoPlasma.Blank.obs: Number of "NoPlasma.Blank" sample types for the tested compound
NoPlasma.Blank.obs: Response of the "NoPlasma.Blank" sample types for the tested compound
NoPlasma.Blank.cal: Indices of the unique Calibration values that corresponds to the "NoPlasma.Blank" sample types' Calibration for the tested compound
NoPlasma.Blank.df: Unique Dilution Factor of the "NoPlasma.Blank" sample types for the tested compound
Num.CC.obs: Number of "CC" sample types with non-NA Test.Compound.Conc values for the tested compound
CC.conc: Test.Compound.Conc (non-NA) of the "CC" sample types for the tested compound
CC.obs: Response of the "CC" sample types with non-NA Test.Compound.Conc for the tested compound
CC.cal: Indices of the unique Calibration values that corresponds to the "CC" sample types' Calibration for the tested compound
CC.df: Unique Dilution Factor of the "NoPlasma.Blank" sample types for the tested compound
Num.T0.obs: Number of "T0" sample types for the tested compound
T0.obs: Response of the "T0" sample types for the tested compound
T0.cal: Indices of the unique Calibration values that corresponds to the "T0" sample types' Calibration for the tested compound
T0.df: Unique Dilution Factor of the "T0" sample types for the tested compound
Num.rep: Unique number of (Calibration + Technical.Replicates) combinations for "PBS" and "Plasma" sample types for the tested compound
Num.PBS.obs: Number of "PBS" sample types for the tested compound
PBS.obs: Response of the "PBS" sample types for the tested compound
PBS.cal: Indices of the unique Calibration values that corresponds to the "PBS" sample types' Calibration for the tested compound
PBS.df: Unique Dilution Factor of the "PBS" sample types for the tested compound
PBS.rep: Integer representing "PBS" replicate group for the tested compound
Num.Plasma.obs: Number of "Plasma" sample types for the tested compound
Plasma.obs: Response of the "Plasma" sample types for the tested compound
Plasma.cal: Indices of the unique Calibration values that corresponds to the "Plasma" sample types' Calibration for the tested compound
Plasma.df: Unique Dilution Factor of the "Plasma" sample types for the tested compound
Plasma.rep: Integer representing "Plasma" replicate group for the tested compound