extractEnzAbund: Extract enzyme abundance data from a simulator output Excel...

In shirewoman2/Consultancy: Standardized tools for using R within the Simcyp Consultancy Team

Extract enzyme abundance data from a simulator output Excel file

Description

Extracts enzyme abundance data from a simulator output Excel file. The appropriate tab must be present in the output file. For detailed instructions and examples, please see the SharePoint file "Simcyp PBPKConsult R Files - Simcyp PBPKConsult R Files/SimcypConsultancy function examples and instructions/Enzyme abundance plots/Enzyme-abundance-plot-examples.docx". (Sorry, we are unable to include a link to it here.)

Usage

extractEnzAbund(
  sim_data_file,
  enzyme = "CYP3A4",
  tissue = "liver",
  returnAggregateOrIndiv = "both",
  existing_exp_details = NA
)

Arguments

sim_data_file	name of the Excel file containing the simulated enzyme-abundance-time data, in quotes
enzyme	the enzyme of interest, e.g., "CYP3A4" (default), "UGT1A1", etc. Spaces or hyphens in enzyme names will be ignored. Not case sensitive.
tissue	From which tissue should the desired enzyme abundance be extracted? Options are "liver" (default), "gut", or "kidney". Note: If "gut" is selected, the output will return both colon and small intestine concentrations.
returnAggregateOrIndiv	Return aggregate and/or individual simulated enzyme abundance data? Options are "individual", "aggregate", or "both" (default). Aggregated data are not calculated here but are pulled from the simulator output rows labeled as "mean".
existing_exp_details	If you have already run extractExpDetails_mult or extractExpDetails to get all the details from the "Input Sheet" (e.g., when you ran extractExpDetails you said exp_details = "Input Sheet" or exp_details = "all"), you can save some processing time by supplying that object here, unquoted. If left as NA, this function will run extractExpDetails behind the scenes to figure out some information about your experimental set up.

Details

Note: Unlike the similar function for extracting drug concentrations, extractConcTime, This has not been set up yet to get the dose number for a custom-dosing regimen.

Value

A data.frame of enzyme abundance with time with the following columns:

Enzyme

the enzyme whose abundance is listed

Tissue

the tissue

Substrate

what the substrate was in the simulation

Inhibitor

what the perpetrator was in the simulation if there was one

Individual

the individual for the given profile, which will be a number for a simulated individual or will be "obs" or "obs+inhibitor" for observed data, "mean" for the mean data, "geomean" for the geometric mean data, or "per5" or "per95" for the 5th and 95th percentile data.

Trial

the trial number for that set of simulations or "obs", "mean", etc. for the observed or aggregate data

Time

the time since the first dose

Abundance

abundance of the enzyme listed

Time_units

units used for time

Dose_num_x

the dose number for the substrate (suffix is "_sub"), inhibitor 1 ("_inhib1"), or inhibitor 2 ("_inhib2")

Dose_int_x

the dosing interval for that compound. This will be NA for custom-dosing regimens.

TimeSinceDose1_x

time since dose 1 for that compound

Examples

extractEnzAbund(sim_data_file = "../Example simulator output MD.xlsx",
                enzyme = "CYP3A4", tissue = "liver")
                
                

shirewoman2/Consultancy documentation built on Feb. 18, 2025, 10 p.m.