Find features using SAFD

Uses SAFD to obtain features. This functionality is still experimental. Please see the details below.

Usage

findFeaturesSAFD(
  analysisInfo,
  prefCentroid = FALSE,
  mzRange = c(0, 400),
  maxNumbIter = 1000,
  maxTPeakW = 300,
  resolution = 30000,
  minMSW = 0.02,
  RThreshold = 0.75,
  minInt = 2000,
  sigIncThreshold = 5,
  S2N = 2,
  minPeakWS = 3,
  centroidMethod = "RFM",
  centroidDM = 0.005,
  verbose = TRUE
)

Arguments

analysisInfo

A data.frame (or data.table) with Analysis information.

prefCentroid

Set to TRUE to prefer centroided data over other MS data specified in analysisInfo.

NOTE: if prefCentroid=FALSE but the package option patRoon.MS.preferIMS=TRUE (see msdata), then centroided data will still be preferred over IMS data.

mzRange

The m/z window to be imported.

maxNumbIter, maxTPeakW, resolution, minMSW, RThreshold, minInt, sigIncThreshold, S2N, minPeakWS

Parameters directly passed to the safd_s3D function.

centroidMethod, centroidDM

Passed to the safd_s3d_cent function (method and mdm arguments, respectively).

verbose

If set to FALSE then no text output is shown.

Value

An object of a class which is derived from features.

Details

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

The support for SAFD is still experimental, and its interface might change in the future.

In order to use SAFD, please make sure that its Julia packages are installed and you have verified that everything works, e.g. by running the test data with SAFD.

As of patRoon 3.0, findFeaturesSAFD uses the msdata interface instead of the MS_Import.jl Julia package to read HRMS data. This means that MS_Import.jl does not need to be installed, and all file formats supported by msdata are also supported for SAFD feature detection. This includes IMS-HRMS data, however, in that case IMS resolved spectra are summed and the IMS dimension is removed to make the data compatible for SAFD.

The SAFD algorithm was primarily developed to detect features in profile m/z data, but centroided data is also supported. To use profile data, ensure that the paths are correctly set up in the analysisInfo. Furthermore, when using profile data you probably also need to specify centroided data in the analysisInfo, as e.g. generateMSPeakLists currently does not support profile data. If IMS-HRMS data is used it is treated as profile data, as this data is typically not or partially centroided (generateMSPeakLists supports IMS-HRMS data directly).

Parallelization

findFeaturesSAFD uses multiprocessing to parallelize computations. Please see the parallelization section in the handbook for more details and patRoon options for configuration options.

Note that for caching purposes, the analyses files must always exist on the local host computer, even if it is not participating in computations.

References

Samanipour S, OBrien JW, Reid MJ, Thomas KV (2019). “Self Adjusting Algorithm for the Nontargeted Feature Detection of High Resolution Mass Spectrometry Coupled with Liquid Chromatography Profile Data.” Analytical Chemistry, 91(16), 10800–10807. doi:10.1021/acs.analchem.9b02422 .