Get or set analysis parameters — parameters • metabolyseR

Get or set parameters for AnalysisParameters or Analysis class objects.

Usage

parameters(d, ...)

# S4 method for AnalysisParameters
parameters(d, element)

# S4 method for Analysis
parameters(d)

parameters(d, element) <- value

# S4 method for AnalysisParameters
parameters(d, element) <- value

# S4 method for Analysis
parameters(d) <- value

Arguments

d: S4 object of class AnalysisParameters or Analysis
...: arguments to pass to the appropriate method
element: analysis element for parameters to extract or assign. Should be one of those returned by analysisElements()
value: list containing parameter values

Examples

p <- analysisParameters('pre-treatment')

## extract pre-treatment parameters
parameters(p,'pre-treatment')
#> $QC
#> $QC$occupancyFilter
#> $QC$occupancyFilter$cls
#> [1] "class"
#> 
#> $QC$occupancyFilter$QCidx
#> [1] "QC"
#> 
#> $QC$occupancyFilter$occupancy
#> 2/3
#> 
#> 
#> $QC$impute
#> $QC$impute$cls
#> [1] "class"
#> 
#> $QC$impute$QCidx
#> [1] "QC"
#> 
#> $QC$impute$occupancy
#> 2/3
#> 
#> $QC$impute$parallel
#> [1] "variables"
#> 
#> $QC$impute$seed
#> [1] 1234
#> 
#> 
#> $QC$RSDfilter
#> $QC$RSDfilter$cls
#> [1] "class"
#> 
#> $QC$RSDfilter$QCidx
#> [1] "QC"
#> 
#> $QC$RSDfilter$RSDthresh
#> [1] 50
#> 
#> 
#> $QC$removeQC
#> $QC$removeQC$cls
#> [1] "class"
#> 
#> $QC$removeQC$QCidx
#> [1] "QC"
#> 
#> 
#> 
#> $occupancyFilter
#> $occupancyFilter$maximum
#> $occupancyFilter$maximum$cls
#> [1] "class"
#> 
#> $occupancyFilter$maximum$occupancy
#> 2/3
#> 
#> 
#> 
#> $impute
#> $impute$class
#> $impute$class$cls
#> [1] "class"
#> 
#> $impute$class$occupancy
#> 2/3
#> 
#> $impute$class$seed
#> [1] 1234
#> 
#> 
#> 
#> $transform
#> $transform$TICnorm
#> $transform$TICnorm$refactor
#> [1] TRUE
#> 
#> 
#> 

## set pre-treatment parameters
parameters(p,'pre-treatment') <- preTreatmentParameters(
  list(
    remove = 'classes',
    QC = c('RSDfilter','removeQC'),
    transform = 'TICnorm'
  )
)

print(p)
#> Parameters:
#> pre-treatment
#> 	remove
#> 		classes
#> 			cls = class
#> 			classes = c()
#> 	QC
#> 		RSDfilter
#> 			cls = class
#> 			QCidx = QC
#> 			RSDthresh = 50
#> 		removeQC
#> 			cls = class
#> 			QCidx = QC
#> 	transform
#> 		TICnorm
#> 			refactor = TRUE
#>