analysis-accessors: 'AnalysisData' and 'Analysis' class accessors

In jasenfinch/metabolyseR: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data

AnalysisData and Analysis class accessors

Description

Accessor methods for the AnalysisData and Analysis S4 classes.

Usage

dat(x, ...)

## S4 method for signature 'AnalysisData'
dat(x)

## S4 method for signature 'Analysis'
dat(x, type = c("pre-treated", "raw"))

dat(x, ...) <- value

## S4 replacement method for signature 'AnalysisData'
dat(x) <- value

## S4 replacement method for signature 'Analysis'
dat(x, type = c("pre-treated", "raw")) <- value

sinfo(x, ...)

## S4 method for signature 'AnalysisData'
sinfo(x)

## S4 method for signature 'Analysis'
sinfo(x, type = c("pre-treated", "raw"), value)

sinfo(x, ...) <- value

## S4 replacement method for signature 'AnalysisData'
sinfo(x) <- value

## S4 replacement method for signature 'Analysis'
sinfo(x, type = c("pre-treated", "raw")) <- value

raw(x)

## S4 method for signature 'Analysis'
raw(x)

raw(x) <- value

## S4 replacement method for signature 'Analysis'
raw(x) <- value

preTreated(x)

## S4 method for signature 'Analysis'
preTreated(x)

preTreated(x) <- value

## S4 replacement method for signature 'Analysis'
preTreated(x) <- value

features(x, ...)

## S4 method for signature 'AnalysisData'
features(x)

## S4 method for signature 'Analysis'
features(x, type = c("pre-treated", "raw"))

nSamples(x, ...)

## S4 method for signature 'AnalysisData'
nSamples(x)

## S4 method for signature 'Analysis'
nSamples(x, type = c("pre-treated", "raw"))

nFeatures(x, ...)

## S4 method for signature 'AnalysisData'
nFeatures(x)

## S4 method for signature 'Analysis'
nFeatures(x, type = c("pre-treated", "raw"))

analysisResults(x, element)

## S4 method for signature 'Analysis'
analysisResults(x, element)

Arguments

x	S4 object of class AnalysisData or Analysis
...	arguments to pass to the appropriate method
type	get or set raw or pre-treated data
value	value to set
element	analysis element results to return

Methods

• dat: Return a metabolomic data table.

• ⁠dat<-⁠: Set a metabolomic data table.

• sinfo: Return a sample information data table.

• ⁠sinfo<-⁠: Set a sample information data table.

• raw: Return the AnalysisData object containing unprocessed metabolomic data from an Analysis object.

• ⁠raw<-⁠: Set an AnalysisData object to the raw slot of an Analysis class object.

• preTreated: Return the AnalysisData object containing pre-treated metabolomic data from an Analysis object.

• ⁠preTreated<-⁠: Set an AnalysisData object to the pre-treated slot of an Analysis class object.

• features: Return the features names.

• nSamples: Return the number of samples.

• nFeatures: Return the number of features.

• analysisResults: Return results from an Analysis object of an analysis element.

Examples

library(metaboData)

d <- analysisData(abr1$neg[,200:300],abr1$fact)

## Return the metabolomic data
dat(d)

## Set the metabolomic data
dat(d) <- abr1$neg[,300:400]

## Return the sample information
sinfo(d)

## Set the sample information
sinfo(d) <- abr1$fact

## Return the feature names
features(d)

## Return the number of samples
nSamples(d)

## Return the number of features
nFeatures(d)

jasenfinch/metabolyseR documentation built on Sept. 18, 2023, 1:25 a.m.