anClique: 'anClique' class constructor

Description Usage Arguments Details Value See Also Examples

View source: R/allClasses.R

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

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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

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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.