bruker-utils: Bruker DataAnalysis utilities

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

Bruker DataAnalysis utilities

Description

Miscellaneous utility functions which interface with Bruker DataAnalysis

Usage

showDataAnalysis()

setDAMethod(anaInfo, method, close = TRUE)

revertDAAnalyses(anaInfo, close = TRUE, save = close)

recalibrarateDAFiles(anaInfo, close = TRUE, save = close)

getDACalibrationError(anaInfo)

addDAEIC(
  analysis,
  path,
  mz,
  mzWindow = 0.005,
  ctype = "EIC",
  mtype = "MS",
  polarity = "both",
  bgsubtr = FALSE,
  fragpath = "",
  name = NULL,
  hideDA = TRUE,
  close = FALSE,
  save = close
)

addAllDAEICs(
  fGroups,
  mzWindow = 0.005,
  ctype = "EIC",
  bgsubtr = FALSE,
  name = TRUE,
  onlyPresent = TRUE,
  hideDA = TRUE,
  close = FALSE,
  save = close
)

Arguments

anaInfo	Analysis info table
method	The full path of the DataAnalysis method.
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.
analysis	Analysis name (without file extension).
path	path of the analysis.
mz	m/z (Da) value used for the chromatographic trace (if applicable).
mzWindow	m/z window (in Da) used for the chromatographic trace (if applicable).
ctype	Type of the chromatographic trace. Valid options are: "EIC" (extracted ion chromatogram), "TIC" (total ion chromatogram, only for addDAEIC) and "BPC" (Base Peak Chromatogram).
mtype	MS filter for chromatographic trace. Valid values are: "all", "MS", "MSMS", "allMSMS" and "BBCID".
polarity	Polarity filter for chromatographic trace. Valid values: "both", "positive" and "negative".
bgsubtr	If TRUE then background subtraction ('Spectral' algorithm) will be performed.
fragpath	Precursor m/z used for MS/MS traces ("" for none).
name	For addDAEIC: the name for the chromatographic trace. For addAllEICs: TRUE to automatically set EIC names. Set to NULL for none.
hideDA	Hides DataAnalysis while adding the chromatographic trace (faster).
fGroups	The featureGroups object for which EICs should be made.
onlyPresent	If TRUE then EICs are only generated for analyses where the feature was detected.

Details

These functions communicate directly with Bruker DataAnalysis to provide various functionality, such as calibrating and exporting data and adding chromatographic traces. For this the RDCOMClient package is required to be installed.

showDataAnalysis makes a hidden DataAnalysis window visible again. Most functions using DataAnalysis will hide the window during processing for efficiency reasons. If the window remains hidden (e.g. because there was an error) this function can be used to make it visible again. This function can also be used to start DataAnalysis if it is not running yet.

setDAMethod Sets a given DataAnalysis method (‘.m’ file) to a set of analyses. NOTE: as a workaround for a bug in DataAnalysis, this function will save(!), close and re-open any analyses that are already open prior to setting the new method. The close argument only controls whether the file should be closed after setting the method (files are always saved).

revertDAAnalyses Reverts a given set of analyses to their unprocessed raw state.

recalibrarateDAFiles Performs automatic mass recalibration of a given set of analyses. The current method settings for each analyses will be used.

getDACalibrationError is used to obtain the standard deviation of the current mass calibration (in ppm).

addDAEIC adds an Extracted Ion Chromatogram (EIC) or other chromatographic trace to a given analysis which can be used directly with DataAnalysis.

addAllDAEICs adds Extracted Ion Chromatograms (EICs) for all features within a featureGroups object.

Value

getDACalibrationError returns a data.frame with a column of all analyses (named analysis) and their mass error (named error).

See Also

analysis-information

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