peakListId: peak list Identification

Description Usage Arguments Value

Description

peak list Identification

Usage

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peakListId(adductSpectra = NULL, peakList = c(290.21, 403.3, 
516.38, 587.42, 849.4, 884.92, 958.46, 993.97, 1050.52, 1107.06,
1209.73, 1337.79,
1465.85), exPeakMass = 834.7769, frag.delta = 1, minPeaksId = 7, 
minSpecEx = 50, maxRtDrift = 360, maxPpmDev = 200, allScans = TRUE, 
closestMassByFile = TRUE, outputPlotDir = NULL)

Arguments

adductSpectra

AdductSpec object param peakList numeric vector of peak masses param exPeakMass numeric internal standard peak mass

peakList

numeric vector of peak masses

exPeakMass

numeric mass of explained peak

frag.delta

integer delta mass accuracy difference.

minPeaksId

numeric minimum number of peaks IDed

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.

maxRtDrift

numeric the maximum retention time drift (in seconds) to identify MS/MS spectrum scans (default = 360). param outputPlotDir character string of output directory (e.g. internal standard IAA-T3 peak list = peakList= 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))

maxPpmDev

numeric ppm deviation

allScans

boolean include all scans

closestMassByFile

boolean closest mass in files

outputPlotDir

character string for output plot directory

Value

dataframe peak list


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