invitroTKstats (version 0.0.14)

create_method_table: Creates a Standardized Data Table for Chemical Analysis Methods

Description

This function extracts the chemical analysis methods from a set of MS data and returns a data frame with each row representing a unique chemical-method pair. (Unique chemical identified by DTXSID.) Each row contains all compound names, analysis parameters, analysis instruments, and internal standards used for each chemical-method pair.

Usage

create_method_table(
  input.table,
  dtxsid.col = "DTXSID",
  compound.col = "Compound.Name",
  istd.name.col = "ISTD.Name",
  analysis.method.col = "Analysis.Method",
  analysis.instrument.col = "Analysis.Instrument",
  analysis.parameters.col = "Analysis.Parameters",
  verbose = TRUE
)

Value

A data frame with one row per chemical-method pair containing information on analysis parameters, instruments, internal standards, and compound identifiers used for each pair.

Arguments

input.table

(Data Frame) A level-1 or level-2 data frame containing mass-spectrometry peak areas, indication of chemical identity, and analytical chemistry methods. It 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".)

istd.name.col

(Character) Column name of input.table containing identity of the internal standard. (Defaults to "ISTD.Name".)

analysis.method.col

(Character) Column name of input.table containing the analytical chemistry analysis method, typically "LCMS" or "GCMS", liquid or gas chromatography mass spectrometry, respectively. (Defaults to "Analysis.Method".)

analysis.instrument.col

(Character) Column name of input.table containing the instrument used for chemical analysis. For example, "Agilent 6890 GC with model 5973 MS". (Defaults to "Analysis.Instrument".)

analysis.parameters.col

(Character) Column name of input.table containing the parameters used to identify the compound on the chemical analysis instrument. For example, "Negative Mode, 221.6/161.6, -DPb=26, FPc=-200, EPd=-10, CEe=-20, CXPf=-25.0". (Defaults to "Analysis.Parameters".)

verbose

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

Author

John Wambaugh

Examples

library(invitroTKstats)
# Smeltz et al. (2020) data:
##  Clint ##
create_method_table(
  input.table = invitroTKstats::clint_L1,
  dtxsid.col = "DTXSID",
  compound.col = "Compound.Name",
  istd.name.col = "ISTD.Name",
  analysis.method.col = "Analysis.Method",
  analysis.instrument.col = "Analysis.Instrument",
  analysis.parameters.col = "Analysis.Parameters"
  )
## Fup RED ##
create_method_table(
  input.table = invitroTKstats::fup_red_L1,
  dtxsid.col = "DTXSID",
  compound.col = "Compound.Name",
  istd.name.col = "ISTD.Name",
  analysis.method.col = "Analysis.Method",
  analysis.instrument.col = "Analysis.Instrument",
  analysis.parameters.col = "Analysis.Parameters"
  )
## Fup UC ##
create_method_table(
  input.table = invitroTKstats::fup_uc_L1,
  dtxsid.col = "DTXSID",
  compound.col = "Compound.Name",
  istd.name.col = "ISTD.Name",
  analysis.method.col = "Analysis.Method",
  analysis.instrument.col = "Analysis.Instrument",
  analysis.parameters.col = "Analysis.Parameters"
  )
# Honda et al. () data:
## Caco2 ##
create_method_table(
  input.table = invitroTKstats::caco2_L1,
  dtxsid.col = "DTXSID",
  compound.col = "Compound.Name",
  istd.name.col = "ISTD.Name",
  analysis.method.col = "Analysis.Method",
  analysis.instrument.col = "Analysis.Instrument",
  analysis.parameters.col = "Analysis.Parameters"
  )