anClique {cliqueMS} | R Documentation

## 'anClique' class constructor

### Description

S4 Class `anClique` 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.

### Usage

    anClique(peaklist = data.frame(),
        network = igraph::make_empty_graph(directed = FALSE),
        cliques = list(), cliquesFound = FALSE, isotopes = data.frame(),
        isoFound = FALSE, anFound = FALSE)

### Arguments

`peaklist` | 'data.frame' with feature and annotation information.
`network` | 'igraph' undirected network of similarity.
`cliques` | list with the groups of features
`cliquesFound` | 'TRUE' if cliques have been computed.
`isotopes` | 'data.frame' with isotope annotation.
`isoFound` | 'TRUE' if isotopes have been computed.
`anFound` | 'TRUE' if annotation has been computed.

### Details

See `help("anClique-class")` for information about the slots and methods of the S4 class 'anClique'.

### Value

A new 'anClique' object with variable values set by the user.

### See Also

`createanClique`

`anClique-class`

### 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]