Pre-treatment parameters

Return pre-treatment elements, methods and parameters.

Usage

preTreatmentElements()

preTreatmentMethods(element)

preTreatmentParameters(methods)

Arguments

element

pre-treatment element name

methods

a named list of element methods

Examples

## Return the availalble pre-treatment elements
preTreatmentElements()
#> [1] "aggregate"       "correction"      "impute"          "keep"           
#> [5] "occupancyFilter" "QC"              "remove"          "transform"      

## Return the available pre-treatment methods for the remove element
preTreatmentMethods('remove')
#> [1] "classes"  "features" "samples" 

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

## Assign the pre-treatment parameters to analysis parameters
ap <- analysisParameters('pre-treatment')
parameters(ap,'pre-treatment') <- p

print(ap)
#> 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
#>