generateComponents: Grouping feature groups in components

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

Grouping feature groups in components

Description

Functionality to automatically group related feature groups (e.g. isotopes, adducts and homologues) to assist and simplify annotation.

Usage

generateComponents(fGroups, algorithm, ...)

## S4 method for signature 'featureGroups'
generateComponents(fGroups, algorithm, ...)

Arguments

fGroups	featureGroups object for which components should be generated.
algorithm	A character string describing the algorithm that should be used: "ramclustr", "camera", "nontarget", "intclust", "openms", "cliquems", "specclust", "tp"
...	Any parameters to be passed to the selected component generation algorithm.

Details

Several algorithms are provided to group feature groups that are related in some (chemical) way to each other. How feature groups are related depends on the algorithm: examples include adducts, statistics and parents/transformation products. The linking of this data is generally useful for annotation purposes and reducing data complexity.

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

Value

A components (derived) object containing all generated components.

Sets workflows

In a sets workflow the componentization data is generated differently depending on the used algorithm. Please see the details in the algorithm specific functions linked in the ⁠See Also⁠ section.

See Also

The components output class and its methods and the algorithm specific functions: generateComponentsRAMClustR, generateComponentsCAMERA, generateComponentsNontarget, generateComponentsIntClust, generateComponentsOpenMS, generateComponentsCliqueMS, generateComponentsSpecClust, generateComponentsTPs

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