updateObject {clusterExperiment} | R Documentation

## 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`

[Package clusterExperiment version 2.7.2 Index]