update2.4.md

New to Version 2.3.0

Change to ClusterExperiment Object

Important If you have objects created since 2.0.0 but with a version < 2.3.0 (i.e. including 2.0.0), you should run updateObject to update the class definition because there have been changes to the class definition since that version:

ceObj<-updateObject(ceObj)

Warning This command will, however, loose information saved about the last mergeClusters call that you have made if your object is from version < 2.1.4. You may want to save that information and manually update the slots. If you do so, make sure you call validObject to make sure that you have done so correctly (in particular, you will have to have a value for the slot merge_demethod, see ?ClusterExperiment which is a new slot). For example,

ceObjNew<-updateObject(ceObj)
ceObjNew@merge_index<-ceObj@merge_index
<etc>

If you have objects from before 2.0.0 (when the class was called 'clusterExperiment'), you should construct a new object using the ClusterExperiment function. For example,

ceObjNew<-ClusterExperiment(
    se=as(ceObj,"SingleCellExperiment"), 
    clusterMatrix=ceObj@clusterMatrix, 
    <etc>
    )

See ?ClusterExperiment for the names of the slots.

Other important changes

There have also been a number of changes and enhancements to the package. These are the most important (a complete list is detailed in the NEWS file of the package -- all releases since May 1, 2018)



epurdom/clusterCells documentation built on April 28, 2024, 8:14 p.m.