gtoxRun: Perform data processing

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

Perform data processing

Description

gtoxRun is the function for performing the data processing, for both single-concentration and multiple-concentration formats.

Usage

gtoxRun(asid = NULL, slvl, elvl, id = NULL, type = "mc",
  mc.cores = NULL, outfile = NULL, runname = NULL)

Arguments

asid	Integer, assay source id
slvl	Integer of length 1, the starting level to process
elvl	Integer of length 1, the ending level to process
id	Integer, rather than assay source id, the specific assay component or assay endpoint id(s) (optional)
type	Character of length 1, the data type, "sc" or "mc"
mc.cores	Integer of length 1, the number of cores to use, set to 1 when using Windows operating system
outfile	Character of length 1, the name of the log file (optional)
runname	Character of length 1, the name of the run to be used in the oufile (optional)

Details

The gtoxRun function is the core processing function within the package. The function acts as a wrapper for individual processing functions, (ie. mc1, sc1, etc.) that are not exported. If possible, the processing is done in parallel by 'id' by utilizing the mclapply function within the parallel package.

If slvl is less than 4, 'id' is interpreted as acid and if slvl is 4 or greater 'id' is interpreted as aeid. Must give either 'asid' or 'id'. If an id fails no results get loaded into the database, and the id does not get placed into the cue for subsequent level processing.

The 'type' parameter specifies what type of processing to complete: "mc" for multiple-concentration processing, and "sc" for single-concentration processing.

Value

A list containing the results from each level of processing. Each level processed will return a named logical vector, indicating the success of the processing for the id.

Examples

## Process data for asid 1

## Process data
gtoxRun(asid = 1L, slvl = 1, elvl = 6, mc.cores = 2)

pmpsa-hpc/GladiaTOX documentation built on Sept. 1, 2023, 5:52 p.m.