getDefAvgPListParams: Parameters for averaging MS peak list data

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Parameters for averaging MS peak list data

Description

Create parameter lists for averaging MS peak list data.

Usage

getDefAvgPListParams(...)

Arguments

...	Optional named arguments that override defaults.

Details

The parameters set used for averaging peak lists are set by the avgFeatParams and avgFGroupParams arguments to generateMSPeakLists and its related algorithm specific functions. The parameters are specified as a named list with the following values:

• clusterMzWindow m/z window (in Da) used for clustering m/z values when spectra are averaged. For method="hclust" this corresponds to the cluster height, while for method="distance" this value is used to find nearby masses (+/- window). Too small windows will prevent clustering m/z values (thus erroneously treating equal masses along spectra as different), whereas too big windows may cluster unrelated m/z values from different or even the same spectrum together.

• topMost Only retain this maximum number of MS peaks when generating averaged spectra. Lowering this number may exclude more irrelevant (noisy) MS peaks and decrease processing time, whereas higher values may avoid excluding lower intense MS peaks that may still be of interest.

• minIntensityPre MS peaks with intensities below this value will be removed (applied prior to selection by topMost) before averaging.

• minIntensityPost MS peaks with intensities below this value will be removed after averaging.

• avgFun Function that is used to calculate average m/z values.

• method Method used for producing averaged MS spectra. Valid values are "hclust", used for hierarchical clustering (using the fastcluster package), and "distance", to use the between peak distance. The latter method may reduces processing time and memory requirements, at the potential cost of reduced accuracy.

• pruneMissingPrecursorMS For MS data only: if TRUE then peak lists without a precursor peak are removed. Note that even when this is set to FALSE, functionality that relies on MS (not MS/MS) peak lists (e.g. formulae calulcation) will still skip calculation if a precursor is not found.

• retainPrecursorMSMS For MS/MS data only: if TRUE then always retain the precursor mass peak even if is not amongst the topMost peaks. Note that MS precursor mass peaks are always kept. Furthermore, note that precursor peaks in both MS and MS/MS data may still be removed by intensity thresholds (this is unlike the filter method function).

The getDefAvgPListParams function can be used to generate a default parameter list. The current defaults are:

clusterMzWindow=0.005; topMost=50; minIntensityPre=500; minIntensityPost=500; avgFun=mean; method="hclust"; pruneMissingPrecursorMS=TRUE; retainPrecursorMSMS=TRUE

Value

getDefAvgPListParams returns a list with the peak list averaging parameters.

Source

Averaging of mass spectra algorithms used by are based on the msProcess R package (now archived on CRAN).

Note

With Bruker algorithms these parameters only control generation of feature groups averaged peak lists: how peak lists for features are generated is controlled by DataAnalysis.

References

\addCitations

fastcluster1

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.