Generate components based on intensity profiles

Generates components based on intensity profiles of feature groups.

Usage

generateComponentsIntClust(fGroups, ...)

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

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.

IMS

(IMS workflow) Specifies which feature groups are considered for componentization in IMS workflows. The following options are valid:

"both": Selects IMS and non-IMS features.
"maybe": Selects non-IMS features and IMS features without assigned IMS precursor.
FALSE: Selects only non-IMS features.
TRUE: Selects only IMS features.

Value

The components are stored in objects derived from componentsIntClust.

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.

IMS workflows

In IMS workflows with post mobility assignment (see assignMobilities) it may be necessary to call expandForIMS when componentization was performed prior to mobility assignments, see its documentation for more details.

If mobilities were already assigned prior to componentization, then the IMS argument selects which feature groups are subjected to componentization. Data for IMS feature groups that were not considered (i.e. when IMS is FALSE or "maybe"), will be expanded similarly as is done by expandForIMS.

Sets workflows

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

References

Müllner D (2013). “fastcluster: Fast Hierarchical, Agglomerative Clustering Routines for R and Python.” Journal of Statistical Software, 53(9), 1–18. doi:10.18637/jss.v053.i09 .

Schollee JE, Bourgin M, von Gunten U, McArdell CS, Hollender J (2018). “Non-target screening to trace ozonation transformation products in a wastewater treatment train including different post-treatments.” Water Research, 142, 267–278. doi:10.1016/j.watres.2018.05.045 .