extractEnzAbund_mult: Pull enzyme-abundance data from multiple Simcyp Simulator...

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

Pull enzyme-abundance data from multiple Simcyp Simulator output files

Description

extractEnzAbund_mult is meant to be used in conjunction with enz_plot_overlay to create graphs from multiple Simcyp Simulator output files or from multiple enzymes or tissues. If you list multiple files, multiple tissues, and/or multiple enzymes to extract (see notes on options below), this will extract all possible variations of them. For example, if you ask for data from the files "sim1.xlsx" and "sim2.xlsx" and then also ask for the enzymes "CYP3A4" and "CYP2C9", you will get the CYP3A4 and CYP2C9 abundance data from both files. NOTE: If ANY of the Excel files you wish to extract data from are open, this WILL CRASH and WILL NOT save whatever progress it has made so far. Be sure to close all of the source Excel files. 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_mult(
  sim_data_files = NA,
  sim_enz_dataframe = NA,
  overwrite = FALSE,
  enzymes = "CYP3A4",
  tissues = "liver",
  time_units_to_use = "hours",
  returnAggregateOrIndiv = "aggregate",
  existing_exp_details = NA,
  fromMultFunction = FALSE,
  ...
)

Arguments

sim_data_files	a character vector of simulator output files, each in quotes and encapsulated with c(...), NA to extract enzyme-abundance data for all the Excel files in the current folder, or "recursive" to extract enzyme-abundance data for all the Excel files in the current folder and all subfolders. Example of acceptable input: c("sim1.xlsx", "sim2.xlsx"). The path should be included with the file names if they are located somewhere other than your working directory. If some of your Excel files are not regular simulator output, e.g. they are sensitivity analyses or a file where you were doing some calculations, those files will be skipped.
sim_enz_dataframe	(optional) a data.frame that contains previously extracted enzyme-abundance data. This should NOT be in quotes. Because we can see scenarios where you might want to extract some enzyme-abundance data, play around with those data, and then later decide you want to pull more enzyme-abundance data for comparisons, this data.frame can already exist. When that is the case, this function will add data to that data.frame. It will not overwrite existing data unless overwrite is set to TRUE.
overwrite	TRUE or FALSE (default) on whether to re-extract the enzyme-abundance data from output files that are already included in sim_enz_dataframe. Since pulling data from Excel files is slow, by default, this will not overwrite existing data and instead will only add data from any Excel files that aren't already included. A situation where you might want to set this to TRUE would be when you have changed input parameters for simulations and re-run them.
enzymes	the enzymes of interest, e.g., "CYP3A4" (default), "UGT1A1", etc. Any enzyme present in the simulator output should work fine. To request multiple enzymes, enclose them in c(...), e.g., enzymes = c("CYP3A4", "CYP2D6", "CYP2C19"). Spaces or hyphens in enzyme names will be ignored. Not case sensitive.
tissues	From which tissues should the desired enzyme abundances be extracted? Options are "liver" (default), "gut", or "kidney". Note: If "gut" is selected, the output will return both colon and small intestine concentrations. To request multiple tissues, enclose them in c(...), e.g., tissues = c("liver", "gut", "kidney")
time_units_to_use	time units to use so that all data will be comparable. Options are "hours" (default) or "minutes".
returnAggregateOrIndiv	Return aggregate and/or individual simulated enzyme-abundance data? Options are "aggregate" (default), "individual", or "both". Aggregated data are not calculated here but are pulled from the simulator output rows labeled as "Population Statistics".
existing_exp_details	If you have already run extractExpDetails_mult to get all the details from the "Input Sheet" (e.g., when you ran extractExpDetails_mult 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.
fromMultFunction	INTERNAL USE ONLY. TRUE or FALSE on whether this is being called on by extractConcTime_mult.

Value

Returns a large data.frame with multiple sets of enzyme-abundance data, formatted the same way as output from the function extractEnzAbund

Examples

ConcTimeData <-
      extractEnzAbund_mult(
            sim_data_files = c("MyFile1.xlsx", "MyFile2.xlsx"),
            overwrite = FALSE,
            enzymes = c("CYP3A4", "CYP2C9"),
            tissues = c("liver", "gut", "kidney"))

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