Create an AnalysisParameters S4 class object

Initiate an AnalysisParameters object with the default analysis parameters for each of the analysis elements.

Usage

analysisParameters(elements = analysisElements())

Arguments

elements

character vector containing elements for analysis.

Value

An S4 object of class AnalysisParameters containing the default analysis parameters.

Examples

p <- analysisParameters()

print(p)
#> Parameters:
#> pre-treatment
#> 	QC
#> 		occupancyFilter
#> 			cls = class
#> 			QCidx = QC
#> 			occupancy = 2/3
#> 		impute
#> 			cls = class
#> 			QCidx = QC
#> 			occupancy = 2/3
#> 			parallel = variables
#> 			seed = 1234
#> 		RSDfilter
#> 			cls = class
#> 			QCidx = QC
#> 			RSDthresh = 50
#> 		removeQC
#> 			cls = class
#> 			QCidx = QC
#> 	occupancyFilter
#> 		maximum
#> 			cls = class
#> 			occupancy = 2/3
#> 	impute
#> 		class
#> 			cls = class
#> 			occupancy = 2/3
#> 			seed = 1234
#> 	transform
#> 		TICnorm
#> 			refactor = TRUE
#> 
#> modelling
#> 	randomForest
#> 		cls = class
#> 		rf = list()
#> 		reps = 1
#> 		binary = FALSE
#> 		comparisons = list()
#> 		perm = 0
#> 		returnModels = FALSE
#> 		seed = 1234
#> 
#> correlations
#> 	method = pearson
#> 	pAdjustMethod = bonferroni
#> 	corPvalue = 0.05
#> 	minCoef = 0
#> 	maxCor = Inf