detectPretreatmentParameters: Detect pre-treatment parameters

Description Usage Arguments Value Examples

Description

Detect pre-treatment parameters for Binalysis or MetaboProfile class objects.

Usage

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detectPretreatmentParameters(x, cls = "class", QCidx = "QC")

## S4 method for signature 'Binalysis'
detectPretreatmentParameters(x, cls = "class", QCidx = "QC")

## S4 method for signature 'MetaboProfile'
detectPretreatmentParameters(x, cls = "class", QCidx = "QC")

Arguments

x

S4 object of class Binalysis, MetaboProfile or AnalysisData

cls

the name of the sample information table column containing the sample class information

QCidx

QC sample class label

Value

S4 object of class AnalysisParameters

Examples

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## Retreive example file paths and sample information 
file_paths <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes') %>% 
   .[61:63]

sample_information <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes') %>% 
    dplyr::filter(name == 'QC01' | name == 'QC02' | name == 'QC03')

## Detect spectral binning parameters
bp <- binneR::detectParameters(file_paths)

## Perform spectral binning
bd <- binneR::binneRlyse(file_paths,sample_information,bp)

## Detect pre-treatment parameters
pp <- detectPretreatmentParameters(bd) 

pp

jasenfinch/metaboMisc documentation built on Feb. 10, 2022, 4:22 p.m.