anClique-class: 'anClique' S4 class for annotating isotopes and adducts

In osenan/cliqueMS: Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

'anClique' S4 class for annotating isotopes and adducts

Description

S4 Class anClique-class for annotating isotopes and adducts in processed m/z data. Features are first grouped based on a similarity network algorithm and then annotation of isotopes and adducts is performed in each group. The class contains the following slots.

Usage

## S4 method for signature 'anClique'
show(object)

## S4 method for signature 'anClique'
getPeaklistanClique(object)

## S4 method for signature 'anClique'
getNetanClique(object)

## S4 method for signature 'anClique'
getIsolistanClique(object)

## S4 method for signature 'anClique'
getlistofCliques(object)

## S4 method for signature 'anClique'
hasAnnotation(object)

## S4 method for signature 'anClique'
hasCliques(object)

## S4 method for signature 'anClique'
hasIsotopes(object)

## S4 replacement method for signature 'anClique'
getIsolistanClique(object) <- value

## S4 replacement method for signature 'anClique'
getNetanClique(object) <- value

## S4 replacement method for signature 'anClique'
getlistofCliques(object) <- value

## S4 replacement method for signature 'anClique'
getPeaklistanClique(object) <- value

## S4 replacement method for signature 'anClique'
hasAnnotation(object) <- value

## S4 replacement method for signature 'anClique'
hasCliques(object) <- value

## S4 replacement method for signature 'anClique'
hasIsotopes(object) <- value

Arguments

object	'anClique' S4 object.
value	Is the new variable which can be a 'peaklist', a 'network', a 'isotopes' a 'cliques' a 'cliquesFound' a 'isoFound' or 'anFound' and it's set by the user.

Value

An 'anClique' object with annotation of isotopes, adducts and fragments, and information about the annotation process.

Methods (by generic)

• show: show information about the object

• getPeaklistanClique: get the list of features with current annotation

• getNetanClique: get the correlation network

• getIsolistanClique: get the table of isotopes

• getlistofCliques: get the list of the clique groups

• hasAnnotation: is 'TRUE' if annotation has been computed

• hasCliques: is 'TRUE' if cliques have been computed

• hasIsotopes: is 'TRUE' if isotopes have been computed

• getIsolistanClique<-: set the table of isotopes

• getNetanClique<-: set the network of correlation

• getlistofCliques<-: set the list of clique groups

• getPeaklistanClique<-: set the list of features

• hasAnnotation<-: set if annotation has been computed

• hasCliques<-: set if cliques have been computed

• hasIsotopes<-: set if isotopes have been computed

Slots

'peaklist'

Is a data.frame with m/z, retention time and intensity information for each feature. It also contains adduct and isotope information if annotation has been performed.

'network'

Is an igraph undirected network of similarity used to compute groups of features before annotation.

'cliques'

Is a list that contains the groups of features. Each id corresponds to a row in the peaklist.

'isotopes'

Is a data.frame with the column 'feature' for feature id, column 'charge' for the charge, column 'grade' that starts with 0 and it is 1 for the first isotope, 2 for the second and so on and column 'cluster' which labels each group of features that are isotopes.

'cliquesFound'

is TRUE if clique groups have been computed,

'isoFound'

is TRUE if isotopes have been annotated,

'anFound'

is TRUE if annotation of adducts have been computed.

See Also

createanClique

Examples

mzfile <- system.file("standards.mzXML", package = "cliqueMS")
library(xcms)
mzraw <- readMSData(files = mzfile, mode = "onDisk")
cpw <- CentWaveParam(ppm = 15, peakwidth = c(5,20), snthresh = 10)
mzData <- findChromPeaks(object = mzraw, param = cpw)
ex.anClique <- createanClique(mzdata = mzData)
show(ex.anClique)

osenan/cliqueMS documentation built on March 15, 2024, 10:06 p.m.