findFeaturesSIRIUS: Find features using SIRIUS

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

Find features using SIRIUS

Description

Uses SIRIUS to find features.

Usage

findFeaturesSIRIUS(analysisInfo, verbose = TRUE)

Arguments

analysisInfo	A data.frame with Analysis information.
verbose	If set to FALSE then no text output is shown.

Details

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

The features are collected by running the lcms-align SIRIUS command for every analysis.

The MS files should be in the ‘mzML’ or ‘mzXML’ format. Furthermore, this algorithms requires the presence of (data-dependent) MS/MS data.

The input MS data files need to be centroided. The convertMSFiles function can be used to centroid data.

Value

An object of a class which is derived from features.

Parallelization

findFeaturesSIRIUS 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

\insertRef

Dhrkop2019patRoon

See Also

findFeatures for more details and other algorithms.

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