anClique: 'anClique' class constructor

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

'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)

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