updateObject: Update an object to its current class definition

Description Usage Arguments Details Value Legacy bcbioRNADataSet class Legacy bcbioRnaseq package Note Author(s) See Also Examples

Description

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

Usage

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## S4 method for signature 'bcbioRNASeq'
updateObject(object, rowRanges = NULL)

Arguments

object

Object to be updated for updateObject and updateObjectFromSlots.

Object for slot information to be extracted from for getObjectSlots.

rowRanges

GRanges or NULL. Row annotations. Since we converted to RangedSummarizedExperiment in v0.2.0, this option had to be added to enable updating of newly required rowRanges slot. Objects that are >= v0.2 don't require this argument and it can be left NULL.

Details

Update old objects created by the bcbioRNASeq package. The session information metadata is preserved from the time when the bcbio data was originally loaded into R.

Value

bcbioRNASeq.

Legacy bcbioRNADataSet class

Support for bcbioRNADataSet objects was dropped in v0.2.0 of the package. If you need to load one of these objects, please install an older release.

Legacy bcbioRnaseq package

The previous bcbioRnaseq package (note case) must be reinstalled to load objects from versions <= 0.0.20. We changed the name of the package to bcbioRNASeq starting in v0.0.21.

Note

Updated 2019-08-12.

Author(s)

Michael Steinbaugh

See Also

Examples

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data(bcb)
updateObject(bcb)

## Example that depends on remote file.
## > x <- import(file.path(bcbioRNASeqTestsURL, "bcbioRNASeq_0.1.4.rds"))
## > x <- updateObject(x)
## > x

hbc/bcbioRNASeq documentation built on Sept. 11, 2019, 5:50 a.m.