anClique-class {cliqueMS} | R Documentation

## '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)

[Package cliqueMS version 1.8.0 Index]