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Extracted Ion Chromatogram and Mobilogram parameters

Source: R/utils-exported.R
EIXParams.Rd

Parameters for creation of extracted ion chromatograms and mobilograms.

Usage

getDefEICParams(...)

getDefEIMParams(..., IMS = getLimIMS())

Arguments

...

optional named arguments that override defaults.

IMS

A character that specifies for which IMS instrument defaults are returned. Should be "bruker" or "agilent". Defaults to what is specified in limits.

Details

The following parameters exist to configure the creation of extracted ion chromatograms (EICs) and extracted ion mobilograms (EIMs):

  • window A value that is subtracted or added to the minimum and maximum retention time (EICs) or mobility (EIMs) of the feature. Thus, setting this value to >0 will 'zoom out' on the x-axis of a chromatogram or mobilogram. Defaults to defaultLim("retention", "wide") (EICs) or defaultLim("mobility", "wide") (EIMs) (see limits). Set to Inf to use the full retention time or mobility range.

  • topMost Only create EICs/EIMs for this number of top most intense features. If NULL then EICs/EIMs are created for all features.

  • topMostByReplicate If set to TRUE and topMost is set: only create EICs/EIMs for the top most features in each replicate. For instance, when topMost=1 and topMostByReplicate=TRUE, then only the most intense feature of each replicate is considered.

  • onlyPresent If TRUE then EICs/EIMs are created only for analyses in which a feature was detected, if onlyPresent=FALSE then data is generated for all analyses. The latter is handy to evaluate if a peak was 'missed' during peak detection or removed during e.g. filtering.

  • mzExpMobWindow (IMS workflow) Additional m/z tolerance on top of the feature limits. This is for IMS workflows where features were detected from centroided LC-MS like data, while EICs/EIMs are generated from raw IMS data. In this case the feature m/z limits were derived from centroided data, which typically has smaller m/z deviations across scans compared to IMS data. The mzExpMobWindow parameter sets an additional m/z tolerance to specifically handle this case. Defaults to defaultLim("mz", "default") (see limits).

  • minIntensityIMS (IMS workflow) Raw intensity threshold for IMS data. This is primarily intended to speed up raw data processing.

if onlyPresent=FALSE then the following parameters are also relevant:

  • mzExpWindow,mobExpWindow To create EICs or EIMs for analyses in which no feature was found, the m/z or mobility value is derived from the min/max values of all features in the feature group. The value of mzExpWindow and mobExpWindow further expands this window to allow a greater tolerance. Defaults to defaultLim("mz", "very_narrow") and defaultLim("mobility", "very_narrow") (see limits).

  • setsAdductPos,setsAdductNeg (sets workflow) In sets workflows the adduct must be known to calculate the ionized m/z. If a feature is completely absent in a particular set then it follows no adduct annotations are available and the value of setsAdductPos (positive ionization data) or setsAdductNeg (negative ionization data) will be used instead.

The following additional parameters exist specifically for EICs (EICParams):

  • gapFactor Bruker TIMS data (and maybe others?) seem to omit zero intensity scans, which will lead to time gaps between spectra and incorrect EICs. To determine a time gap, the gapFactor is multiplied with the median of time differences between scans. If a gap is detected, then appropriate zero intensity points are added to the EIC. Set to 0 to disable this.

The following additional parameters exist specifically for EIMs (EIMParams):

  • maxRTWindow Maximum retention time window (seconds, +/- feature retention time) in which mobilograms are collected and averaged. Defaults to defaultLim("retention", "very_narrow") (see limits).

  • smooth The smoothing method that is applied to the EIM. Can be "none" for no smoothing, "sg" for Savitzky-Golay (using signal)) or "ma" for centered moving average (same algorithm as used by findFeaturesPiek).

  • smLength The smoothing length. If smooth="sg" then this is passed as the n argument to the signal::sgolayfilt function.

  • sgOrder The smoothing order for Savitzky-Golay. Passed as the p argument to the signal::sgolayfilt function.

These parameters are passed as a named list as the EICParams or EIMParams argument to functions that work with EIC or EIM data. The getDefEICParams and getDefEIMParams functions generate such parameter list with defaults.