findFeatures: Finding features

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

Finding features

Description

Automatically find features.

Usage

findFeatures(analysisInfo, algorithm, ..., verbose = TRUE)

Arguments

analysisInfo	A data.frame with Analysis information.
algorithm	A character string describing the algorithm that should be used: "bruker", "openms", "xcms", "xcms3", "envipick", "sirius", "kpic2", "safd"
...	Further parameters passed to the selected feature finding algorithms.
verbose	If set to FALSE then no text output is shown.

Details

Several functions exist to collect features (i.e. retention and MS information that represent potential compounds) from a set of analyses. All 'feature finders' return an object derived from the features base class. The next step in a general workflow is to group and align these features across analyses with groupFeatures. Note that some feature finders have a plethora of options which sometimes may have a large effect on the quality of results. Fine-tuning parameters is therefore important, and the optimum is largely dependent upon applied analysis methodology and instrumentation.

findFeatures is a generic function that will find features by one of the supported algorithms. The actual functionality is provided by algorithm specific functions such as findFeaturesOpenMS and findFeaturesXCMS. While these functions may be called directly, findFeatures provides a generic interface and is therefore usually preferred.

Value

An object of a class which is derived from features.

Note

In most cases it will be necessary to centroid your MS input files. The only exception is Bruker, however, you will still need centroided ‘mzXML’/‘mzML’ files for e.g. plotting chromatograms. In this case the centroided MS files should be stored in the same directory as the raw Bruker ‘.d’ files. The convertMSFiles function can be used to centroid data.

See Also

The features output class and its methods and the algorithm specific functions: findFeaturesBruker, findFeaturesOpenMS, findFeaturesXCMS, findFeaturesXCMS3, findFeaturesEnviPick, findFeaturesSIRIUS, findFeaturesKPIC2, findFeaturesSAFD

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