adductSpecGen: Constructor of AdductSpec object deconvolute spectra MS2 and...
In JosieLHayes/adductomicsR: Processing of adductomic mass spectral datasets

Description Usage Arguments Value

reads mzXML files from a directory extracts metadata info, groups ion signals with signalGrouping, filters noise dynamically dynamicNoiseFilter and identifies precursor ion charge state, by isotopic pattern.

adductSpecGen(mzXmlDir=NULL, runOrder=NULL, nCores=NULL,
intStdMass=834.77692,intStdPeakList=c(290.21, 403.30, 516.38,
587.42,849.40, 884.92, 958.46, 993.97,1050.52, 1107.06, 1209.73,
1337.79,1465.85),TICfilter=10000, DNF=2, minInt=300,
minPeaks=5,intStd_MaxMedRtDrift=360, intStd_MaxPpmDev=200,minSpecEx=40,
outputPlotDir=NULL)

`mzXmlDir`	character a full path to a directory containing either .mzXML or .mzML data
`runOrder`	character a full path to a csv file specifying the runorder for each of the files the first column must contain the precise file name and the second column an integer representing the precise run order.
`nCores`	numeric the number of cores to use for parallel computation. The default is to 1 core
`intStdMass`	numeric vector of the mass of the internal standard. Default is the mass of
`intStdPeakList`	numeric vector of masses for the internal standard peaks
`TICfilter`	numeric minimimum total ion current of an MS/MS scan. Any MS/MS scan below this value will be filtered out (default=0).
`DNF`	dynamic noise filter minimum signal to noise threshold (default = 2), calculated as the ratio between the linear model predicted intensity value and the actual intensity.
`minInt`	numeric minimum intensity value
`minPeaks`	minimum number of signal peaks following dynamic noise filtration (default = 5).
`intStd_MaxMedRtDrift`	numeric the maximum retention time drift window (in seconds) to identify internal standard MS/MS spectrum scans (default = 600).
`intStd_MaxPpmDev`	numeric the maximum mass accuracy window (in ppm). to identify internal standard MS/MS spectrum scans (default = 200 ppm).
`minSpecEx`	numeric the minimum percentage of the total ion current explained by the internal standard fragments (default = 40). Sometime spectra are not identified due to this cutoff being set too high. If unexpected datapoints have been interpolated then reduce this value.
`outputPlotDir`	character string for the output directory for plots, default is working directory.