Evaluate the Kramer model for chemical distribution in vitro. Takes input as data table or vectors of values. Outputs a data table.
kramer_eval(
chem.cas = NULL,
chem.name = NULL,
dtxsid = NULL,
casrn.vector = NA_character_,
nomconc.vector = 1,
this.well_number = 384,
tcdata = NA,
user_assay_parameters = NA,
this.serum = NA_real_,
this.csalt = 0.15,
this.BSA = 44,
this.v_total = NA_real_,
this.v_working = NA_real_,
this.cell_yield = NA_real_,
this.L_per_mil_cells = 2.772e-06,
this.sarea = NA_real_,
this.Tsys = 37,
this.Tref = 298.15,
this.temp_k = 298.15,
this.prot_conc = 0.21,
this.option.bottom = TRUE,
restrict.ion.partitioning = FALSE,
surface.area.switch = TRUE
)| Input Parameter | Description | Units |
| concentration_cells | Concentration in cells | uM |
| concentration_medium | Concentration in medium | uM |
| concentration_plastic | Concentration in plastic | umol/m^2 |
| concentration_air | Concentration in headspace | uM |
A single or vector of Chemical Abstracts Service Registry Number(s) (CAS-RN) of desired chemical(s).
A single or vector of name(s)) of desired chemical(s).
A single or vector ofEPA's DSSTox Structure ID(s) (https://comptox.epa.gov/dashboard)
A deprecated argument specifying a single or vector of Chemical Abstracts Service Registry Number(s) (CAS-RN) of desired chemical(s).
For vector or single value, micromolar (uM = mol/L) nominal concentration (e.g. AC50 value)
For single value, plate format default is 384, used
if is.na(tcdata)==TRUE. This value chooses default surface area settings for
armitage_estimate_sarea based on the number of wells per plate.
A data.table with casrn, nomconc,v_total, v_working. Otherwise supply single values to this.params (e.g., this.sarea,
this.v_total, etc.). Chemical parameters are taken from
chem.physical_and_invitro.data.
option to fill in your own assay parameters (data table)
Concentration of serum in media (percent volume/volume)
Ionic strength of buffer, mol/L
Bovine serum albumin concentration in serum (g/L)
Total volume of well (uL)
Volume of medium per well (uL)
Number of cells/well seeded (unitless)
Liters per 1 million cells
Surface area of plastic exposed to medium (m^2)
System temperature (Celcius)
Reference temperature (Kelvin)
Temperature (Kelvin)
Cell protein concentration (mg protein/million cells)
Include the bottom of the well in surface area calculation
only allow neutral fraction to partition
TRUE, automatically calculates surface area, switch to FALSE if user provided
description
description
Nominal test concentration (uM)
Meredith Scherer, adapted from code written by L.S Lautz for A. Punt, N. Kramer
kramer2010measuringhttk