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

Description Usage Arguments Value Methods (by generic) Slots See Also Examples

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

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## 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)

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

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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 Aug. 6, 2020, 5:52 a.m.