adductSpecGen: Constructor of AdductSpec object deconvolute spectra MS2 and...

Description Usage Arguments Value

Description

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.

Usage

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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)

Arguments

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.

Value

AdductSpec object


JosieLHayes/adductomicsR documentation built on May 5, 2019, 9:43 p.m.