updateObject: Update old ClusterExperiment object to current class...

In epurdom/clusterExperiment: Compare Clusterings for Single-Cell Sequencing

Update old ClusterExperiment object to current class definition

Description

This function updates ClusterExperiment objects from previous versions of package into the current definition

Usage

## S4 method for signature 'ClusterExperiment'
updateObject(object, checkTransformAndAssay = FALSE, ..., verbose = FALSE)

Arguments

object	a ClusterExperiment (or clusterExperiment from older versions). Must have at a minimum a slot clusterMatrix.
checkTransformAndAssay	logical. Whether to check the content of the assay and given transformation function for whether they are valid.
...	Additional arguments, for use in specific updateObject methods.
verbose	TRUE or FALSE, indicating whether information about the update should be reported. Use message to report this information.

Details

The function creates a valid ClusterExperiment object by adding the default values of missing slots. It does so by calling the ClusterExperiment function, which imputs default (empty) values for missing slots.

The object is required to have minimal components to be updated. Specifically, it must have all the required elements of a Summarized Experiment as well as the basic slots of a ClusterExperiment object which have not changed over time. These are: clusterMatrix, primaryIndex, clusterInfo, transformation, clusterTypes, clusterLegend, orderSamples.

If any of the dendrogram-related slots are missing, ALL of the dendrogram and merge related slots will be cleared to default values. Similarly, if any of the merge-related slots are missing, ALL of the merge-related slots will be cleared to the default values.

Cluster and Sample dendrograms of the class dendrogram will be updated to the phylo4d class now used in ClusterExperiment objects; the merge information on these nodes will be updated to have the correct format (i.e. match to the internal node id names in the new dendrogram). The previous identification of nodes that was previously created internally by plotDendrogram and the merging (labels in the form of 'Node1','Node2'), will be kept as nodeLabels in the new dendrogram class.

The function currently only works for object of ClusterExperiment, not the older name clusterExperiment.

Value

A valid ClusterExperiment object based on the current definition of ClusterExperiment.

See Also

ClusterExperiment

epurdom/clusterExperiment documentation built on April 28, 2024, 8:17 p.m.