Detect modelling parameters

Detect suitable modelling parameters for Binalysis, MetaboProfile or Analysis S4 classes.

Usage

detectModellingParameters(x, ...)

# S4 method for Binalysis
detectModellingParameters(x)

# S4 method for MetaboProfile
detectModellingParameters(x)

# S4 method for Analysis
detectModellingParameters(x, type = "pre-treated", cls = "class")

Arguments

x

an object of S4 class Binalysis,MetaboProfile or Analysis

...

arguments to pass to the appropriate method

type

detect modelling parameters for raw or pre-treated data for the Analysis S4 class

cls

sample information column to use as the response for modelling

Value

and object of S4 class AnalysisParameters

Examples

## Retrieve file paths and sample information for example data
files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')

info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')

## Perform spectral binning
analysis <- binneR::binneRlyse(files, 
                               info, 
                               parameters = binneR::detectParameters(files))
#> binneR v2.6.3 Fri Jul 21 17:26:36 2023
#> ________________________________________________________________________________
#> Scans: 5:13 
#> ________________________________________________________________________________
#> Reading raw data
#> Gathering bins
#> Removing single scan events
#> Averaging intensities across scans
#> Calculating bin metrics
#> Calculating accurate m/z
#> Building intensity matrix
#> Gathering file headers
#> 
#> Completed! [39.5S]

## Detect modelling parameters
modelling_parameters <- detectModellingParameters(analysis)

modelling_parameters
#> Parameters:
#> modelling
#> 	randomForest
#> 		cls = class
#> 		rf = list()
#> 		reps = 10
#> 		binary = FALSE
#> 		comparisons = list()
#> 		perm = 0
#> 		returnModels = FALSE
#> 		seed = 1234
#>