invitroTKstats (version 0.0.14)

summarize_table: Creates a Summary Table of Mass-Spectrometry (MS) Data

Description

This function creates and returns a list containing summary counts from the provided data frame containing mass-spectrometry (MS) data, MS calibration, chemical identifiers, and measurement type. The list includes the number of observations, unique chemicals, unique measurements in the input data table, and a vector of chemicals that have repeated observations. If a vector of data types is specified in the argument req.types, the function also checks if each chemical has observations for every measurement type included in the vector for each chemical-calibration pair. If it does, the chemical is said to have a complete data set. Otherwise, it has an incomplete data set. The number of complete and incomplete datasets, for each chemical, are returned in the output list. The input data frame can be level-1 (or level-2) Caco-2 data, ultracentrifugation (UC) data, rapid equilibrium dialysis (RED) data, or hepatocyte clearance (Clint) data. See the Details section for measurement type and annotation tables used in each assay.

Usage

summarize_table(
  input.table,
  dtxsid.col = "DTXSID",
  compound.col = "Compound.Name",
  cal.col = "Calibration",
  type.col = "Sample.Type",
  req.types = NULL,
  verbose = TRUE
)

Value

A list containing the summary counts from the input data table. The list includes the number of observations, the number of unique chemicals, the number of unique measurements, the number of chemicals with complete data sets, the number of chemicals with incomplete data sets, and the number of chemicals with repeated observations.

Arguments

input.table

(Data Frame) A data frame (level-1 or level-2) containing mass-spectrometry peak areas, indication of chemical identity, and measurement type. The data frame should contain columns with names specified by the following arguments:

dtxsid.col

(Character) Column name of input.table containing EPA's DSSTox Structure ID (http://comptox.epa.gov/dashboard). (Defaults to "DTXSID".)

compound.col

(Character) Column name of input.table containing the test compound. (Defaults to "Compound.Name".)

cal.col

(Character) Column name of input.table containing the MS calibration. Calibration typically uses indices or dates to represent if the analyses were done on different machines on the same day or on different days with the same MS analyzer. (Defaults to "Calibration".)

type.col

(Character) Column name of input.table containing the sample type (see tables in Details). (Defaults to "Sample.Type".)

req.types

(Character Vector) A vector of character strings containing measurement types. If a vector is specified, each chemical-calibration pair will be checked if it has observations for all of the measurement types in the vector. (Defaults to NULL.)

verbose

(logical) Indicate whether printed statements should be shown. (Default is TRUE.)

Author

John Wambaugh

Details

Sample types used in ultracentrifugation (UC) data collected for calculation of chemical fraction unbound in plasma (Fup) should be annotated as follows:

Calibration Curve

CC

Ultracentrifugation Aqueous Fraction

AF

Whole Plasma T1h Sample

Samples types used in rapid equilibrium dialysis (RED) data collected for calculation of chemical fraction unbound in plasma (Fup) should be annotated as follows:

No Plasma Blank (no chemical, no plasma)	NoPlasma.Blank	Plamsa Blank (no chemical, just plasma)	Plasma.Blank	Plasma well concentration
Plasma	Phosphate-buffered well concentration	PBS	Time zero plasma concentration	T0
Plasma stability sample	Stability	Acceptor compartment of the equilibrium evaluation	EC_acceptor	Donor compartment of the equilibrium evaluation (chemical spiked side)

Sample types in hepatocyte clearance (Clint) data should be annotated as follows:

Blank

Blank

Hepatocyte incubation concentration

Cvst

Inactivated Hepatocytes

Samples types used in Caco-2 data to calculate membrane permeability should be annotated as follows:

Blank with no chemical added	Blank
Target concentration added to donor compartment at time 0 (C0)	D0
Donor compartment at end of experiment	D2
Receiver compartment at end of experiment	R2

Examples

library(invitroTKstats)
# Smeltz et al. (2020) data:
##  Clint ##
summarize_table(
  input.table = invitroTKstats::clint_L2,
  req.types = c("Blank", "Cvst")
  )
## Fup RED ##
summarize_table(
  input.table = invitroTKstats::fup_red_L2,
  req.types=  c("Plasma", "PBS", "Plasma.Blank", "NoPlasma.Blank")
  )
## Fup UC ##
summarize_table(
  input.table = invitroTKstats::fup_uc_L2,
  req.types = c("CC", "T1", "T5", "AF")
  )
# Honda et al. () data:
## Caco2 ##
summarize_table(
  input.table = invitroTKstats::caco2_L2,
  req.types=c("Blank","D0","D2","R2")
  )