invitroTKstats (version 0.0.14)

calc_clint_point: Calculate a Point Estimate of Intrinsic Hepatic Clearance (Clint) (Level-3)

Description

This function calculates a point estimate of intrinsic hepatic clearance (Clint) using mass spectrometry (MS) peak area data collected as part of in vitro measurements of chemical clearance, as characterized by the disappearance of parent compound over time when incubated with primary hepatocytes shibata2002predictioninvitroTKstats.

Usage

calc_clint_point(
  FILENAME,
  data.in,
  good.col = "Verified",
  output.res = FALSE,
  sig.figs = 3,
  INPUT.DIR = NULL,
  OUTPUT.DIR = NULL,
  verbose = TRUE
)

Value

A level-3 data frame with one row per chemical, contains a point estimate of intrinsic clearance (Clint), estimates of Clint of assays performed at 1 and 10 uM (if tested), the p-value and the Akaike Information Criterion (AIC) of the linear regression fit for all chemicals in the input data frame.

Arguments

FILENAME

A string used to identify the input level-2 file, "<FILENAME>-Clint-Level2.tsv" (if importing from a .tsv file), and/or used to identify the output level-3 file, "<FILENAME>-Clint-Level3.tsv" (if exporting).

data.in

(Data Frame) A level-2 data frame generated from the format_clint function with a verification column added by sample_verification. Complement with manual verification if needed.

good.col

(Character) Column name indicating which rows have been verified, data rows valid for analysis are indicated with a "Y". (Defaults to "Verified".)

output.res

(Logical) When set to TRUE, the result table (level-3) will be exported to the user's per-session temporary directory or OUTPUT.DIR (if specified) as a .tsv file. (Defaults to FALSE.)

sig.figs

(Numeric) The number of significant figures to round the exported result table (level-3). (Note: console print statements are also rounded to specified significant figures.) (Defaults to 3.)

INPUT.DIR

(Character) Path to the directory where the input level-2 file exists. If NULL, looking for the input level-2 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.)

Author

John Wambaugh

Details

The input to this function should be "level-2" data. Level-2 data is level-1, data formatted with the format_clint function, and curated with a verification column. "Y" in the verification column indicates the data row is valid for analysis.

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

Blank

Blank

Hepatocyte incubation concentration vs. time

Cvst

Clint is calculated using lm to perform a linear regression of MS response as a function of time.

If the output level-3 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/blog/posts/2023-10-24-til-temp-directories/.

As a best practice, INPUT.DIR (when importing a .tsv file) 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.

References

shibata2002predictioninvitroTKstats

Examples

## Load example level-2 data
level2 <- invitroTKstats::clint_L2

## scenario 1: 
## input level-2 data from the R session and do not export the result table
level3 <- calc_clint_point(data.in = level2, output.res = FALSE)

## scenario 2: 
## import level-2 data from a 'tsv' file and export the result table to 
## same location as INPUT.DIR 
if (FALSE) {
## Refer to sample_verification help file for how to export level-2 data to a directory.
## Unless a different path is specified in OUTPUT.DIR,
## the result table will be saved to the directory specified in INPUT.DIR.
## Will need to replace FILENAME and INPUT.DIR with name prefix and location of level-2 'tsv'.
level3 <- calc_clint_point(# e.g. replace with "Examples" from "Examples-Clint-Level2.tsv"
                           FILENAME="",
                           INPUT.DIR = "",
                           output.res = TRUE)
}

## scenario 3: 
## input level-2 data from the R session and export the result table to the 
## user's temporary directory
## Will need to replace FILENAME with desired level-2 filename prefix. 
if (FALSE) {
level3 <- calc_clint_point(# e.g. replace with "MYDATA"
                           FILENAME = "",
                           data.in = level2,
                           output.res = TRUE)
# To delete, use the following code. For more details, see the link in the 
# "Details" section. 
file.remove(list.files(tempdir(), full.names = TRUE, 
pattern = "-Clint-Level3.tsv"))
}