format_clint: Creates a Standardized Data Frame with Hepatocyte Clearance...

In invitroTKstats: In Vitro Toxicokinetic Data Processing and Analysis Pipeline

Creates a Standardized Data Frame with Hepatocyte Clearance Data (Level-1)

Description

This function formats data describing mass spectrometry (MS) peak areas from samples collected as part of in vitro measurements of chemical stability when incubated with suspended hepatocytes \insertCiteshibata2002predictioninvitroTKstats. Disappearance of the chemical over time is assumed to be due to metabolism by the hepatocytes. The input data frame is organized into a standard set of columns and is written to a tab-separated text file.

Usage

format_clint(
  FILENAME = "MYDATA",
  data.in,
  sample.col = "Lab.Sample.Name",
  date = NULL,
  date.col = "Date",
  compound.col = "Compound.Name",
  dtxsid.col = "DTXSID",
  lab.compound.col = "Lab.Compound.Name",
  type.col = "Sample.Type",
  density = NULL,
  density.col = "Hep.Density",
  cal = NULL,
  cal.col = "Cal",
  dilution = NULL,
  dilution.col = "Dilution.Factor",
  time = NULL,
  time.col = "Time",
  istd.col = "ISTD.Area",
  istd.name = NULL,
  istd.name.col = "ISTD.Name",
  istd.conc = NULL,
  istd.conc.col = "ISTD.Conc",
  test.conc = NULL,
  test.conc.col = "Test.Compound.Conc",
  test.nominal.conc = NULL,
  test.nominal.conc.col = "Test.Target.Conc",
  area.col = "Area",
  biological.replicates = NULL,
  biological.replicates.col = "Biological.Replicates",
  technical.replicates = NULL,
  technical.replicates.col = "Technical.Replicates",
  analysis.method = NULL,
  analysis.method.col = "Analysis.Method",
  analysis.instrument = NULL,
  analysis.instrument.col = "Analysis.Instrument",
  analysis.parameters = NULL,
  analysis.parameters.col = "Analysis.Parameters",
  note.col = "Note",
  level0.file = NULL,
  level0.file.col = "Level0.File",
  level0.sheet = NULL,
  level0.sheet.col = "Level0.Sheet",
  output.res = FALSE,
  save.bad.types = FALSE,
  sig.figs = 5,
  INPUT.DIR = NULL,
  OUTPUT.DIR = NULL,
  verbose = TRUE
)

Arguments

FILENAME	(Character) A string used to identify the output level-1 file. "<FILENAME>-Clint-Level1.tsv", and/or used to identify the input level-0 file, "<FILENAME>-Clint-Level0.tsv" if importing from a .tsv file. (Defaults to "MYDATA").
data.in	(Data Frame) A level-0 data frame or a matrix 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:
sample.col	(Character) Column name of data.in containing the unique mass spectrometry (MS) sample name used by the laboratory. (Defaults to "Lab.Sample.Name".)
date	(Character) The laboratory measurement date, format "MMDDYY" where "MM" = 2 digit month, "DD" = 2 digit day, and "YY" = 2 digit year. (Defaults to NULL.) (Note: Single entry only, use only if all data were collected on the same date.)
date.col	(Character) Column name containing date information. (Defaults to "Date".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in date.)
compound.col	(Character) Column name of data.in containing the test compound. (Defaults to "Compound.Name".)
dtxsid.col	(Character) Column name of data.in containing EPA's DSSTox Structure ID (http://comptox.epa.gov/dashboard). (Defaults to "DTXSID".)
lab.compound.col	(Character) Column name of data.in containing the test compound name used by the laboratory. (Defaults to "Lab.Compound.Name".)
type.col	(Character) Column name of data.in containing the sample type (see table under Details). (Defaults to "Sample.Type".)
density	(Numeric) The density (units of millions of hepatocytes per mL) hepatocytes in the in vitro incubation. (Defaults to NULL.) (Note: Single entry only, use only if all tested compounds have the same density.)
density.col	(Character) Column name containing density information. (Defaults to "Hep.Density".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in density.)
cal	(Character) MS calibration the samples were based on. Typically, this 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 NULL.) (Note: Single entry only, use only if all data were collected based on the same calibration.)
cal.col	(Character) Column name containing cal information. (Defaults to "Cal".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in cal.)
dilution	(Numeric) Number of times the sample was diluted before MS analysis. (Defaults to NULL.) (Note: Single entry only, use only if all samples underwent the same number of dilutions.)
dilution.col	(Character) Column name containing dilution information. (Defaults to "Dilution.Factor".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in dilution.)
time	(Numeric) Time of the measurement (in minutes) since the test chemicals was introduced into the hepatocyte incubation. (Defaults to NULL.) (Note: Single entry only, use only if all measurements were taken after the same amount of time.)
time.col	(Character) Column name containing time information. (Defaults to "Time".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in time.)
istd.col	(Character) Column name of data.in containing the MS peak area for the internal standard. (Defaults to "ISTD.Area".)
istd.name	(Character) The identity of the internal standard. (Defaults to NULL.) (Note: Single entry only, use only if all tested compounds use the same internal standard.)
istd.name.col	(Character) Column name containing istd.name information. (Defaults to "ISTD.Name".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in istd.name.)
istd.conc	(Numeric) The concentration for the internal standard. (Defaults to NULL.) (Note: Single entry only, use only if all tested compounds have the same internal standard concentration.)
istd.conc.col	(Character) Column name containing istd.conc information. (Defaults to "ISTD.Conc".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in istd.conc.)
test.conc	(Numeric) The standard test chemical concentration for the intrinsic clearance assay. (Defaults to NULL.) (Note: Single entry only, use only if the same standard concentration was used for all tested compounds.)
test.conc.col	(Character) Column name containing test.conc information. (Defaults to "Test.Compound.Conc".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in test.conc.)
test.nominal.conc	(Numeric) The nominal concentration added to the well at time 0. (Defaults to NULL.) (Note: Single entry only, use only if all tested compounds used the same concentration at time 0.)
test.nominal.conc.col	(Character) Column name containing test.nominal.conc information. (Defaults to "Test.Target.Conc".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in test.nominal.conc.)
area.col	(Character) Column name of data.in containing the target analyte (that is, the test compound) MS peak area. (Defaults to "Area".)
biological.replicates	(Character) Replicates with the same analyte. Typically, this uses numbers or letters to index. (Defaults to NULL.) (Note: Single entry only, use only if none of the test compounds have replicates.)
biological.replicates.col	(Character) Column name of data.in containing the number or the indices of replicates with the same analyte. (Defaults to "Biological.Replicates".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in biological.replicates.)
technical.replicates	(Character) Repeated measurements from one sample. Typically, this uses numbers or letters to index. (Defaults to NULL.) (Note: Single entry only, use only if none of the test compounds have replicates.)
technical.replicates.col	(Character) Column name of data.in containing the number or the indices of replicates taken from the one sample. (Defaults to "Technical.Replicates".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in technical.replicates.)
analysis.method	(Character) The analytical chemistry analysis method, typically "LCMS" or "GCMS", liquid chromatography or gas chromatography–mass spectrometry, respectively. (Defaults to NULL.) (Note: Single entry only, use only if the same method was used for all tested compounds.)
analysis.method.col	(Character) Column name containing analysis.method information. (Defaults to "Analysis.Method".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in analysis.method.)
analysis.instrument	(Character) The instrument used for chemical analysis, for example "Waters Xevo TQ-S micro (QEB0036)". (Defaults to NULL.) (Note: Single entry only, use only if the same instrument was used for all tested compounds.)
analysis.instrument.col	(Character) Column name containing analysis.instrument information. (Defaults to "Analysis.Instrument".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in analysis.instrument.)
analysis.parameters	(Numeric) The parameters used to identify the compound on the chemical analysis instrument. (Defaults to NULL.) (Note: Single entry only, use only if the same parameters were used for all tested compounds.)
analysis.parameters.col	(Character) Column name containing analysis.parameters information. (Defaults to "Analysis.Parameters".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in analysis.parameters.)
note.col	(Character) Column name of data.in containing additional notes on test compounds. (Defaults to "Note").
level0.file	(Character) The level-0 file from which the data.in were obtained. (Defaults to NULL.) (Note: Single entry only, use only if all rows in data.in were obtained from the same level-0 file.)
level0.file.col	(Character) Column name containing level0.file information. (Defaults to "Level0.File".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in level0.file.)
level0.sheet	(Character) The specific sheet name of level-0 file from which the data.in is obtained from, if the level-0 file is an Excel workbook. (Defaults to NULL.) (Note: Single entry only, use only if all rows in data.in were obtained from the same sheet in the same level-0 file.)
level0.sheet.col	(Character) Column name containing level0.sheet information. (Defaults to "Level0.Sheet".) (Note: data.in does not necessarily have this field. If this field is missing, it can be auto-filled with the value specified in level0.sheet.)
output.res	(Logical) When set to TRUE, the result table (level-1) will be exported to the user's per-session temporary directory or OUTPUT.DIR (if specified) as a .tsv file. (Defaults to FALSE.)
save.bad.types	(Logical) When set to TRUE, export data removed due to inappropriate sample types. See the Detail section for the required sample types. (Defaults to FALSE.)
sig.figs	(Numeric) The number of significant figures to round the exported result table (level-1). (Defaults to 5.)
INPUT.DIR	(Character) Path to the directory where the input level-0 file exists. If NULL, looking for the input level-0 file in the current working directory. (Defaults to NULL.)
OUTPUT.DIR	(Character) Path to the directory to save the output file. If NULL, the output file will be saved to the user's per-session temporary directory or INPUT.DIR if specified. (Defaults to NULL.)
verbose	(logical) Indicate whether printed statements should be shown. (Default is TRUE.)

Details

The data frame of observations should be annotated according to these types:

Blank	Blank
Hepatocyte incubation concentration	Cvst
Inactivated Hepatocytes	Inactive
Calibration Curve	CC

Chemical concentration is calculated qualitatively as a response and returned as a column in the output data frame:

Response <- AREA / ISTD.AREA * ISTD.CONC

If the output level-1 result table is chosen to be exported and an output directory is not specified, it will be exported to the user's R session temporary directory. This temporary directory is a per-session directory whose path can be found with the following code: tempdir(). For more details, see https://www.collinberke.com/til/posts/2023-10-24-temp-directories/.

As a best practice, INPUT.DIR and/or OUTPUT.DIR should be specified to simplify the process of importing and exporting files. This practice ensures that the exported files can easily be found and will not be exported to a temporary directory.

NOTE: For the estimation of Cl~int~ the 'test.conc' and 'test.conc.col' are not used within the calculations currently. However, to maintain consistency with other assays and for the use case that a calibration curve may be part of the estimation in future this was retained. We suggest that if the users do not have a corresponding compound column to set 'test.conc' to 'NA' or use the next most appropriate value/level-0 column name.

Value

A level-1 data frame with a standardized format containing a standardized set of columns and column names with hepatic clearance data for a variety of chemicals.

Author(s)

John Wambaugh

References

\insertRef

shibata2002predictioninvitroTKstats

Examples

## Load the example level-0 data
level0 <- invitroTKstats::clint_L0

## Run it through level-1 processing function
## This example shows the use of the data.in argument which allows users to pass
## in a data frame from the R session.
## If the input level-0 data exists in an external file such as a .tsv file,
## users may import it using INPUT.DIR to specify the path and FILENAME
## to specify the file name. See documentation for details.
level1 <- format_clint(data.in = level0,
                       sample.col ="Sample",
                       date.col="Date",
                       compound.col="Compound",
                       lab.compound.col="Lab.Compound.ID",
                       type.col="Type",
                       dilution.col="Dilution.Factor",
                       cal=1,
                       istd.conc = 10/1000,
                       istd.col= "ISTD.Peak.Area",
                       area.col = "Peak.Area",
                       density = 0.5,
                       test.nominal.conc = 1,
                       biological.replicates = 1,
                       test.conc.col="Compound.Conc",
                       time.col = "Time",
                       analysis.method = "LCMS",
                       analysis.instrument = "Unknown",
                       analysis.parameters.col = "Analysis.Params",
                       note="Sample Text",
                       output.res = FALSE
                       )

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