export_feature_similarity: Extract and export mutual correlation between features.

Description

Extract and export mutual correlation between features in a familiarCollection.

Usage

export_feature_similarity(
  object,
  dir_path = NULL,
  aggregate_results = TRUE,
  feature_cluster_method = waiver(),
  feature_linkage_method = waiver(),
  feature_cluster_cut_method = waiver(),
  feature_similarity_threshold = waiver(),
  export_dendrogram = FALSE,
  export_ordered_data = FALSE,
  export_clustering = FALSE,
  export_collection = FALSE,
  ...
)
# S4 method for familiarCollection
export_feature_similarity(
  object,
  dir_path = NULL,
  aggregate_results = TRUE,
  feature_cluster_method = waiver(),
  feature_linkage_method = waiver(),
  feature_cluster_cut_method = waiver(),
  feature_similarity_threshold = waiver(),
  export_dendrogram = FALSE,
  export_ordered_data = FALSE,
  export_clustering = FALSE,
  export_collection = FALSE,
  ...
)
# S4 method for ANY
export_feature_similarity(
  object,
  dir_path = NULL,
  aggregate_results = TRUE,
  feature_cluster_method = waiver(),
  feature_linkage_method = waiver(),
  feature_cluster_cut_method = waiver(),
  feature_similarity_threshold = waiver(),
  export_dendrogram = FALSE,
  export_ordered_data = FALSE,
  export_clustering = FALSE,
  export_collection = FALSE,
  ...
)

Value

A list containing a data.table (if dir_path is not provided), or nothing, as all data is exported to csv files.

Arguments

object

A familiarCollection object, or other other objects from which a familiarCollection can be extracted. See details for more information.

dir_path

Path to folder where extracted data should be saved. NULL will allow export as a structured list of data.tables.

aggregate_results

Flag that signifies whether results should be aggregated for export.

feature_cluster_method

The method used to perform clustering. These are the same methods as for the cluster_method configuration parameter: none, hclust, agnes, diana and pam.

none cannot be used when extracting data regarding mutual correlation or feature expressions.

If not provided explicitly, this parameter is read from settings used at creation of the underlying familiarModel objects.

feature_linkage_method

The method used for agglomerative clustering in hclust and agnes. These are the same methods as for the cluster_linkage_method configuration parameter: average, single, complete, weighted, and ward.

If not provided explicitly, this parameter is read from settings used at creation of the underlying familiarModel objects.

feature_cluster_cut_method

The method used to divide features into separate clusters. The available methods are the same as for the cluster_cut_method configuration parameter: silhouette, fixed_cut and dynamic_cut.

silhouette is available for all cluster methods, but fixed_cut only applies to methods that create hierarchical trees (hclust, agnes and diana). dynamic_cut requires the dynamicTreeCut package and can only be used with agnes and hclust.

If not provided explicitly, this parameter is read from settings used at creation of the underlying familiarModel objects.

feature_similarity_threshold

The threshold level for pair-wise similarity that is required to form feature clusters with the fixed_cut method.

If not provided explicitly, this parameter is read from settings used at creation of the underlying familiarModel objects.

export_dendrogram

Add dendrogram in the data element objects.

export_ordered_data

Add feature label ordering to data in the data element objects.

export_clustering

Add clustering information to data.

export_collection

(optional) Exports the collection if TRUE.

...

Arguments passed on to as_familiar_collection

familiar_data_names: Names of the dataset(s). Only used if the object parameter is one or more familiarData objects.

collection_name

Name of the collection.

Details

Data is usually collected from a familiarCollection object. However, you can also provide one or more familiarData objects, that will be internally converted to a familiarCollection object. It is also possible to provide a familiarEnsemble or one or more familiarModel objects together with the data from which data is computed prior to export. Paths to the previous files can also be provided.

All parameters aside from object and dir_path are only used if object is not a familiarCollection object, or a path to one.