FEMsettings {metaMS} | R Documentation

## Example settings for `metaMS`

### Description

Examples of settings needed for functions `runLC` and `runGC`: Synapt.RP, Synapt.NP, TSQXLS.GC and Orbitrap.RP. These four particular settings are fine-tuned for the analysis of LC-MS runs, both normal-phase and reverse-phase chromatography (Waters Synapt G1-Thermo Orbitrap)and GC-MS experiments (ThermoXLS TQQ).

### Usage

    data(FEMsettings)

### Format

Four objects of class `metaMSsettings`.

### Author(s)

Ron Wehrens and Pietro Franceschi

### See Also

`findPeaks`, `annotate`

### Examples

    ## Not run:
    ## The three sets of settings are created as follows:
    Synapt.NP <- metaMSsettings(protocolName = "Synapt.QTOF.NP",
                                chrom = "LC",
                                PeakPicking = list(
                                  method = "matchedFilter",
                                  step = 0.05,
                                  fwhm = 20,
                                  snthresh = 4,
                                  max = 50),
                                Alignment = list(
                                  min.class.fraction = .3,
                                  min.class.size = 3,
                                  mzwid = 0.1,
                                  bws = c(130, 10),
                                  missingratio = 0.2,
                                  extraratio = 0.1,
                                  Retcor = list(
                                    method = "linear",
                                    family = "symmetric"),
                                  fillPeaks = TRUE),
                                CAMERA = list(
                                  perfwhm = 0.6,
                                  cor_eic_th = 0.7,
                                  ppm= 5))
    metaSetting(Synapt.NP, "match2DB") <- list(
                rtdiff = 1.5,
                rtval = .1,
                mzdiff = 0.005,
                ppm = 5,
                minfeat = 2)
    metaSetting(Synapt.NP, "DBconstruction") <- list(
                minfeat = 3,
                rttol = .3,
                mztol = .01)

    ## For reverse-phase LC, settings are very similar: the only difference
    ## is in the alignment settings
    Synapt.RP <- Synapt.NP
    metaSetting(Synapt.RP, "protocolName") <- "Synapt.QTOF.RP"
    metaSetting(Synapt.RP, "Alignment") <- list(
                min.class.fraction = .3,
                min.class.size = 3,
                mzwid = 0.1,
                bws = c(30, 10),
                missingratio = 0.2,
                extraratio = 0.1,
                Retcor = list(
                  method = "linear",
                  family = "symmetric"),
                fillPeaks = TRUE)

    ## For the orbitrap.RP
    Orbitrap.RP <- metaMSsettings(protocolName = "Orbitrap",
                                  chrom = "LC",
                                   PeakPicking = list(
                                     method = "centWave",
                                     ppm = 5,
                                     prefilter = c(3,10000),
                                     peakwidth = c(15,40)),
                                 Alignment = list(
                                     bws = 30,
                                     min.class.fraction = 0.3,
                                     min.class.size = 3,
                                     mzwid = 0.01,
                                     Retcor = list(
                                      method = "obiwarp",
                                      profStep = 0.2),
                                     fillPeaks = TRUE),
                                 CAMERA = list(
                                     perfwhm = 0.6,
                                     cor_eic_th = 0.7,
                                     ppm = 5))
    metaSetting(Orbitrap.RP, "match2DB") <- list(
                rtdiff = 1.5,
                rtval = .1,
                mzdiff = 0.005,
                ppm = 5,
                minfeat = 2)
    metaSetting(Orbitrap.RP, "DBconstruction") <- list(
                minfeat = 3,
                rttol = .3,
                mztol = .01)

    ## For the thermo TQ

    TSQXLS.GC <- metaMSsettings("protocolName" = "TSQXLS.QQQ.GC",
                                "chrom" = "GC",
                                PeakPicking = list(
                                  method = "matchedFilter",
                                  step = 0.5,
                                  steps = 2,
                                  mzdiff = .5,
                                  fwhm = 5,
                                  snthresh = 2,
                                  max = 500),
                               CAMERA = list(perfwhm = 1))
    metaSetting(TSQXLS.GC, "DBconstruction") <- list(
                minintens = 0.0,
                rttol = .1,
                intensityMeasure = "maxo",
                DBthreshold = .80,
                minfeat = 5)
    metaSetting(TSQXLS.GC, "match2DB") <- list(
                simthresh = 0.80,
                timeComparison = "rt",
                rtdiff = .5,
                RIdiff = 5,
                minfeat = 2)
    metaSetting(TSQXLS.GC, "matchIrrelevants") <- list(
                irrelevantClasses = c("Bleeding", "Plasticizers"),
                timeComparison = "rt",
                RIdiff = 2,
                rtdiff = .05,
                simthresh = 0.70)
    metaSetting(TSQXLS.GC, "betweenSamples") <- list(
                min.class.fraction = .5,
                min.class.size = 5,
                timeComparison = "rt",
                rtdiff = .05,
                RIdiff = 2,
                simthresh = .95)

    ## End(Not run)

[Package metaMS version 1.24.0 Index]