createanClique: 'createanClique' generic function to create an object of...

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

Description

createanClique creates an 'anClique' object from processed m/z data.e

Usage

createanClique(mzdata)

## S4 method for signature 'xcmsSet'
createanClique(mzdata)

## S4 method for signature 'XCMSnExp'
createanClique(mzdata)

Arguments

mzdata

An object with processed m/z data. See methods for valid class types.

Value

An 'anClique' S4 object with all elements to perform clique grouping, isotope annotation and adduct annotation.

Methods (by class)

• xcmsSet: Method for 'xcmsSet' object

• XCMSnExp: Method for 'XCMSnExp' object

See Also

anClique

Examples

## Using a 'XCMSnExp' object
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)

## Using a 'xcmsSet' object
mzfile <- system.file("standards.mzXML", package = "cliqueMS")
msSet <- xcms::xcmsSet(files = mzfile, method = "centWave",
ppm = 15, peakwidth = c(5,20), snthresh = 10)
ex.anClique <- createanClique(msSet)

cliqueMS documentation built on Nov. 8, 2020, 7:36 p.m.