Import analysis parameters from a .yaml format file or export an AnalysisParameters object to .yaml format.
Usage
parseParameters(path)
exportParameters(d, file = "analysis_parameters.yaml")
# S4 method for AnalysisParameters
exportParameters(d, file = "analysis_parameters.yaml")
# S4 method for Analysis
exportParameters(d, file = "analysis_parameters.yaml")Arguments
- path
file path of .yaml file to parse
- d
S4 object of class AnalysisParameters or Analysis
- file
File name and path to export to
Examples
## Import analysis parameters
paramFile <- system.file('defaultParameters.yaml',package = 'metabolyseR')
p <- parseParameters(paramFile)
p
#> Parameters:
#> pre-treatment
#> QC
#> occupancyFilter
#> cls = class
#> QCidx = QC
#> occupancy = 0.6666667
#> impute
#> cls = class
#> QCidx = QC
#> occupancy = 0.6666667
#> parallel = variables
#> seed = 1234
#> RSDfilter
#> cls = class
#> QCidx = QC
#> RSDthresh = 50
#> removeQC
#> cls = class
#> QCidx = QC
#> occupancyFilter
#> maximum
#> cls = class
#> occupancy = 0.6666667
#> impute
#> class
#> cls = class
#> occupancy = 0.6666667
#> seed = 1234
#> transform
#> TICnorm
#>
#> 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
if (FALSE) {
## Export analysis parameters
exportParameters(p,file = 'analysis_parameters.yaml')
}