peakListId {adductomicsR} | R Documentation

## peak list Identification

### 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

[Package adductomicsR version 1.0.0 Index]