peakListId: peak list Identification

In JosieLHayes/adductomicsR: Processing of adductomic mass spectral datasets

Description

peak list Identification

Usage

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.