fup_red_PREJAGS: Fup RED Level-4 PREJAGS arguments

fup_red_PREJAGSR 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

References

\insertRef

waters2008validationinvitroTKstats

\insertRef

smeltz2023plasmainvitroTKstats


invitroTKstats documentation built on Aug. 23, 2025, 9:08 a.m.