updateObject is a generic function that returns an instance of object updated to its current class definition.

# S4 method for DESeqAnalysis
updateObject(object)

Arguments

object

Object to be updated for updateObject and updateObjectFromSlots.

Object for slot information to be extracted from for getObjectSlots.

Value

DESeqAnalysis.

Details

Updating objects is primarily useful when an object has been serialized (e.g., stored to disk) for some time (e.g., months), and the class definition has in the mean time changed. Because of the changed class definition, the serialized instance is no longer valid.

updateObject requires that the class of the returned object be the same as the class of the argument object, and that the object is valid (see validObject). By default, updateObject has the following behaviors:

updateObject(ANY, …, verbose=FALSE)

By default, updateObject uses heuristic methods to determine whether the object should be the `new' S4 type (introduced in R 2.4.0), but is not. If the heuristics indicate an update is required, the updateObjectFromSlots function tries to update the object. The default method returns the original S4 object or the successfully updated object, or issues an error if an update is required but not possible. The optional named argument verbose causes a message to be printed describing the action. Arguments are passed to updateObjectFromSlots.

updateObject(list, …, verbose=FALSE)

Visit each element in list, applying updateObject(list[[elt]], …, verbose=verbose).

updateObject(environment, …, verbose=FALSE)

Visit each element in environment, applying updateObject(environment[[elt]], …, verbose=verbose)

updateObject(formula, …, verbose=FALSE)

Do nothing; the environment of the formula may be too general (e.g., R_GlobalEnv) to attempt an update.

updateObject(envRefClass, …, verbose=FALSE)

Attempt to update objects from fields using a strategy like updateObjectFromSlots Method 1.

updateObjectFromSlots(object, objclass=class(object), …, verbose=FALSE) is a utility function that identifies the intersection of slots defined in the object instance and objclass definition. Under Method 1, the corresponding elements in object are then updated (with updateObject(elt, …, verbose=verbose)) and used as arguments to a call to new(class, …), with replaced by slots from the original object. If this fails, then Method 2 tries new(class) and assigns slots of object to the newly created instance.

getObjectSlots(object) extracts the slot names and contents from object. This is useful when object was created by a class definition that is no longer current, and hence the contents of object cannot be determined by accessing known slots.

DESeqAnalysis

In the v0.1.8 update, we improved the class to contain Annotated virtual class, which adds support for the metadata() slot. Objects saved by older package versions must be updated to account for this change.

See also

  • updateObjectTo in the Biobase package for updating an object to the class definition of a template (might be useful for updating a virtual superclass).

  • validObject for testing the validity of an object.

  • showMethods for displaying a summary of the methods defined for a given generic function.

  • selectMethod for getting the definition of a specific method.

  • BiocGenerics for a summary of all the generics defined in the BiocGenerics package.

Examples

data(deseq) updateObject(deseq)
#> DESeqAnalysis 0.1.22; DESeq2 1.22.2 #> data: #> dim: 500 12 #> metadata(3): version date interestingGroups #> assays(4): counts mu H cooks #> rownames(500): gene001 gene002 ... gene499 gene500 #> rowData names(27): geneID geneName ... deviance maxCooks #> colnames(12): sample01 sample02 ... sample11 sample12 #> colData names(2): condition sizeFactor #> transformType: varianceStabilizingTransformation #> resultsNames: condition_B_vs_A #> alpha: 0.1 #> lfcThreshold: 0 #> lfcShrinkType: apeglm