QuICSeedR (version 0.1.2)

BulkProcessing: Processing and analyzing Multiple Experiments

Description

This function processes multiple experiments in parallel, performing a series of operations including time conversion, metadata cleaning, raw data cleaning, calculations, analysis, and result summarization.

Usage

BulkProcessing(data, do_analysis = TRUE, params = list(), verbose = FALSE)

Value

A list containing three elements:

• combined_calculation: A data frame of combined calculations from all experiments

• combined_cleanraw: Cleaned raw data for each experiment

• combined_result: A data frame of combined results from all experiments

Arguments

data

Compiled data of experiments.

do_analysis

Logical. Whether statistic analysis is included. Default is TRUE.

params

A list of parameters for various processing steps. If a parameter is not provided, default values will be used. control used in GetAnalysis() is required. parameters can be provided for the following functions:

• ConvertTime

• CleanMeta

• CleanRaw

• GetCalculation

• SpreadCalculation

• GetAnalysis

• SummarizeResult

verbose

Logical; if TRUE, prints detailed processing information for troubleshooting. Default is FALSE.

Examples

#Get path for example data
path = system.file("extdata", package = "QuICSeedR")

#Helper function
add_underscore <- function(text) {
  gsub("([a-zA-Z])(\\d)", "\\1_\\2", text)
  }
  
#Read in data
elkear = BulkReadMARS(path = path, 
                      plate_subfix = 'plate',
                      raw_subfix = 'raw', 
                      helper_func = add_underscore)
                      
#Set up parameters for batch analysis
params = list(
  CleanMeta = list(split_content = TRUE, split_into = c('region', 'sample')),
  GetCalculation = list(cycle_background = 5, norm = TRUE, norm_ct = 'Pos',
                       sd_fold = 10, time_skip = 5),
  GetAnalysis = list(control = "Neg")
  )
  
#Get results     
results = BulkProcessing(data =elkear, params = params)

str(results)