metaMSsettings-class: Class '"metaMSsettings"'

In yguitton/metaMS: MS-based metabolomics annotation pipeline

Class "metaMSsettings"

Description

This class contains all settings needed to run the metaMS pipelines for LC-MS (runLC) and GC-MS (runGC). Slots PeakPicking, Alignment and CAMERA are simply handed over to the appropriate xcms and CAMERA functions; all other slots contain settings for metaMS functions.

Objects from the Class

Objects can be created by calls of the form metaMSsettings(...). See the example below.

Slots

Note: all slots describing retention times or retention time differences use minutes and not seconds. If a slot is only relevant for either GCMS or LCMS, this is indicated explicitly.

protocolName:

Object of class "character": the name of the instrumental protocol, a unique identifier.

chrom:

Object of class "character": chromatography. Either "LC" or "GC".

PeakPicking:

Object of class "list": The parameters used for xcms peakpicking. See the arguments of findPeaks.

Alignment:

Object of class "list": The parameters used for grouping and alignment. min.class.fraction and min.class.size are used to calculate the minsample xcms parameter. bws is a vector of the two bandwidths used for grouping before and after retention time alignent. missingratio and extraratio are used to set the values for missing and extra as a function of the number of samples. LC only.

CAMERA:

Object of class "list": The parameters for CAMERA.

match2DB.rtdiff:

Object of class "numeric": the maximal difference in retention time to match each feature with the entry in the DB.

match2DB.minfeat:

Object of class "numeric": for LC, the minimal number of matching features within a retention time interval of width rtval before we speak of a hit. For GC, the minimal number of common masses for calculating a match factor.

match2DB.rtval:

Object of class "numeric": the tolerance in retention time for features used in annotation. LC only.

match2DB.mzdiff:

Object of class "numeric": the mass accuracy which is used if no error surface is provided. LC only.

match2DB.ppm:

Object of class "numeric": the minimum mass tolerance allowed when the error surface is used. LC only.

match2DB.simthresh:

Object of class "numeric": the minimal match factor to speak of a hit. GC only.

match2DB.timeComparison:

Object of class "character": either "rt" or "RI". GC only.

match2DB.RIdiff:

Object of class "numeric": maximal retention index difference with DB entry (GC only).

DBconstruction.minfeat:

Object of class "numeric": the minimum number of features necessary to include a compound in the DB.

DBconstruction.rttol:

Object of class "numeric": the tolerance in retention time to match experimental features with the reference table.

DBconstruction.mztol:

Object of class "numeric": the tolerance in m/z (in dalton) to match experimental features with the reference table. LC only.

DBconstruction.minintens:

Object of class "numeric": the minimum intensity for a feature to be included in the list. GC only.

DBconstruction.intensityMeasure:

Object of class "character": either "into" or "maxo". GC only.

DBconstruction.DBthreshold:

Object of class "numeric": minimal match factor with an external DB for a pseudospectrum to be included in the DB of standards. GC only.

matchIrrelevants.irrelevantClasses:

Object of class "character": classes of compounds are considered as irrelevant (a vector of string constants, which should exactly match the Class element in the DB entries). GC only.

matchIrrelevants.simthresh:

Object of class "numeric": the minimal match factor to speak of a hit. GC only.

matchIrrelevants.timeComparison:

Object of class "character": either "rt" or "RI". GC only.

matchIrrelevants.rtdiff:

Object of class "numeric": maximal retention time difference between two unknowns - this can be set to a very high value if a pattern is to be removed whatever the retention time. GC only.

matchIrrelevants.RIdiff:

Object of class "numeric": maximal retention index difference between two unknowns - this can be set to a very high value if a pattern is to be removed whatever the Retention Index. GC only.

betweenSamples.min.class.fraction:

Object of class "numeric": fraction of samples in which a pseudospectrum is present before it is regarded as an unknown. GC only.

betweenSamples.min.class.size:

Object of class "numeric": absolute number of samples in which a pseudospectrum is present before it is regarded as an unknown. GC only.

betweenSamples.timeComparison:

Object of class "character": either "rt" or "RI". GC only.

betweenSamples.rtdiff:

Object of class "numeric": max retention time difference between pseudospectra in different samples. GC only.

betweenSamples.RIdiff:

Object of class "numeric": max retention index difference between pseudospectra in different samples. GC only.

betweenSamples.simthresh:

Object of class "numeric": similarity threshold fo comparing pseudospectra in different samples. GC only.

Methods

metaSetting<-

signature(object = "metaMSsettings"): change values in a metaMSsettings object.

metaSetting

signature(object = "metaMSsettings"): get values from a metaMSsettings object.

show

signature(object = "metaMSsettings"): show a metaMSsettings object.

Author(s)

Ron Wehrens

See Also

FEMsettings

Examples

showClass("metaMSsettings")

## 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,
                              retcormethod = "linear",
                              retcorfamily = "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)

## End(Not run)

yguitton/metaMS documentation built on Feb. 27, 2023, 11:45 p.m.