generateComponentsIntClust: Generate components based on intensity profiles

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

Generate components based on intensity profiles

Description

Generates components based on intensity profiles of feature groups.

Usage

generateComponentsIntClust(fGroups, ...)

## S4 method for signature 'featureGroups'
generateComponentsIntClust(
  fGroups,
  method = "complete",
  metric = "euclidean",
  normalized = TRUE,
  average = TRUE,
  maxTreeHeight = 1,
  deepSplit = TRUE,
  minModuleSize = 1
)

Arguments

fGroups	featureGroups object for which components should be generated.
...	Any parameters to be passed to the selected component generation algorithm.
method	Clustering method that should be applied (passed to fastcluster::hclust).
metric	Distance metric used to calculate the distance matrix (passed to daisy).
normalized, average	Passed to as.data.table to perform normalization and averaging of data.
maxTreeHeight, deepSplit, minModuleSize	Arguments used by cutreeDynamicTree.

Details

This function uses hierarchical clustering of intensity profiles to generate components. This function is called when calling generateComponents with algorithm="intclust".

Hierarchical clustering is performed on normalized (and optionally replicate averaged) intensity data and the resulting dendrogram is automatically cut with cutreeDynamicTree. The distance matrix is calculated with daisy and clustering is performed with fastcluster::hclust. The clustering of the resulting components can be further visualized and modified using the methods defined for componentsIntClust.

Value

The components are stored in objects derived from componentsIntClust.

Sets workflows

In a sets workflow normalization of feature intensities occur per set.

References

\addCitations

fastcluster1

\insertRef

Scholle2018patRoon

See Also

generateComponents for more details and other algorithms.

rickhelmus/patRoon documentation built on April 25, 2024, 8:15 a.m.