export: Export results

In jasenfinch/metaboMisc: Miscellaneous Functions for Metabolomics Analyses

Export results

Description

Export data tables from Binalysis,MetaboProfile, Analysis and Assignment classes.

Usage

exportData(x, outPath = ".", ...)

## S4 method for signature 'Binalysis'
exportData(x, outPath = ".")

## S4 method for signature 'MetaboProfile'
exportData(x, outPath = ".")

## S4 method for signature 'AnalysisData'
exportData(x, outPath = ".", idx = "name", prefix = "analysis")

## S4 method for signature 'Analysis'
exportData(x, outPath = ".", type = "raw", idx = "name")

## S4 method for signature 'Assignment'
exportData(x, outPath = ".")

exportSampleInfo(x, outPath = ".", ...)

## S4 method for signature 'Binalysis'
exportSampleInfo(x, outPath = ".")

## S4 method for signature 'MetaboProfile'
exportSampleInfo(x, outPath = ".")

## S4 method for signature 'AnalysisData'
exportSampleInfo(x, outPath = ".", prefix = "analysis")

## S4 method for signature 'Analysis'
exportSampleInfo(x, outPath = ".", type = "raw")

exportAccurateData(x, outPath = ".")

## S4 method for signature 'Binalysis'
exportAccurateData(x, outPath = ".")

exportPeakInfo(x, outPath = ".")

## S4 method for signature 'MetaboProfile'
exportPeakInfo(x, outPath = ".")

exportModellingMetrics(x, outPath = ".")

## S4 method for signature 'Analysis'
exportModellingMetrics(x, outPath = ".")

exportModellingImportance(x, outPath = ".")

## S4 method for signature 'Analysis'
exportModellingImportance(x, outPath = ".")

exportModelling(x, outPath = ".")

## S4 method for signature 'Analysis'
exportModelling(x, outPath = ".")

exportCorrelations(x, outPath = ".")

## S4 method for signature 'Analysis'
exportCorrelations(x, outPath = ".")

exportAssignments(x, outPath = ".")

## S4 method for signature 'Assignment'
exportAssignments(x, outPath = ".")

exportSummarisedAssignments(x, outPath = ".")

## S4 method for signature 'Assignment'
exportSummarisedAssignments(x, outPath = ".")

exportConstruction(x, outPath = ".")

## S4 method for signature 'Construction'
exportConstruction(x, outPath = ".")

exportSummarisedConstruction(x, outPath = ".")

## S4 method for signature 'Construction'
exportSummarisedConstruction(x, outPath = ".")

export(x, outPath = ".", ...)

## S4 method for signature 'Binalysis'
export(x, outPath = ".")

## S4 method for signature 'MetaboProfile'
export(x, outPath = ".")

## S4 method for signature 'AnalysisData'
export(x, outPath = ".", idx = "name", prefix = "analysis")

## S4 method for signature 'Analysis'
export(x, outPath = ".", type = "raw", idx = "name")

## S4 method for signature 'Assignment'
export(x, outPath = ".")

## S4 method for signature 'Construction'
export(x, outPath = ".")

Arguments

x	S4 object of class Binalysis, MetaboProfile, Analysis or Assignment,
outPath	directory path to export to.
...	arguments to pass to relevant method
idx	sample information column name to use as sample IDs
prefix	file name prefix description
type	data type to extract. raw or pre-treated

Value

A character vector of exported file paths.

Examples

## Retrieve file paths and sample information for example data
files <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes')[1:2]

info <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')[1:2,]

## Perform spectral binning
analysis <- binneR::binneRlyse(files, 
                               info, 
                               parameters = binneR::detectParameters(files))

## Export spectrally binned data
export(analysis,outPath = tempdir())

## Perform data pre-treatment and modelling
p <- metabolyseR::analysisParameters(c('pre-treatment','modelling'))
metabolyseR::parameters(p,'pre-treatment') <- metabolyseR::preTreatmentParameters(
   list(occupancyFilter = 'maximum',
        transform = 'TICnorm')
)
metabolyseR::parameters(p,'modelling') <- metabolyseR::modellingParameters('anova')
metabolyseR::changeParameter(p,'cls') <- 'day'
analysis <- metabolyseR::metabolyse(metaboData::abr1$neg[,1:200],
                      metaboData::abr1$fact,
                      p)
                      
## Export pre-treated data and modelling results
export(analysis,outPath = tempdir())

## Perform molecular formula assignment
future::plan(future::sequential)
p <- assignments::assignmentParameters('FIE-HRMS')
assignments <- assignments::assignMFs(assignments::feature_data,p)

## Export molecular formula assignment results
export(assignments,outPath = tempdir())

## Perform consensus structural classification
structural_classifications <- construction::construction(assignments)

## Export consensus structural classification results
export(structural_classifications,outPath = tempdir())

jasenfinch/metaboMisc documentation built on July 31, 2023, 2:28 a.m.