findFeaturesBruker: Find features using Bruker DataAnalysis

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

Find features using Bruker DataAnalysis

Description

Uses the 'Find Molecular Features' (FMF) algorithm of Bruker DataAnalysis vendor software to find features.

Usage

findFeaturesBruker(
  analysisInfo,
  doFMF = "auto",
  startRange = 0,
  endRange = 0,
  save = TRUE,
  close = save,
  verbose = TRUE
)

Arguments

analysisInfo	A data.frame with Analysis information.
doFMF	Run the 'Find Molecular Features' algorithm before loading compounds. Valid options are: "auto" (run FMF automatically if current results indicate it is necessary) and "force" (run FMF always, even if cached results exist). Note that checks done if doFMF="auto" are fairly simplistic, hence set doFMF="force" if feature data needs to be updated.
startRange, endRange	Start/End retention range (seconds) from which to collect features. A 0 (zero) for endRange marks the end of the analysis.
close, save	If TRUE then Bruker files are closed and saved after processing with DataAnalysis, respectively. Setting close=TRUE prevents that many analyses might be opened simultaneously in DataAnalysis, which otherwise may use excessive memory or become slow. By default save is TRUE when close is TRUE, which is likely what you want as otherwise any processed data is lost.
verbose	If set to FALSE then no text output is shown.

Details

This function uses Bruker to automatically find features. This function is called when calling findFeatures with algorithm="bruker".

The resulting 'compounds' are transferred from DataAnalysis and stored as features.

This algorithm only works with Bruker data files (.d extension) and requires Bruker DataAnalysis and the RDCOMClient package to be installed. Furthermore, DataAnalysis combines multiple related masses in a feature (e.g. isotopes, adducts) but does not report the actual (monoisotopic) mass of the feature. Therefore, it is simply assumed that the feature mass equals that of the highest intensity mass peak.

Value

An object of a class which is derived from features.

Note

If any errors related to DCOM appear it might be necessary to terminate DataAnalysis (note that DataAnalysis might still be running as a background process). The ProcessCleaner application installed with DataAnalayis can be used for this.

See Also

findFeatures for more details and other algorithms.

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