updateObject: Update object

In hbc/bcbioRNASeq: Bcbio RNA-Seq

Update object

Description

Update object

Usage

updateObject(object, ..., verbose = FALSE)

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

Arguments

object	Object.
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.
...	Additional arguments.
verbose	logical(1). Run the function with verbose output.

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

Modified object.

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 2023-10-05.

Author(s)

Michael Steinbaugh

Examples

data(bcb)

## bcbioRNASeq ====
object <- bcb
object <- updateObject(object)
validObject(object)

## Example that depends on remote file.
object <- pipette::import(file.path(
    bcbioRnaSeqTestsUrl,
    "bcbioRNASeq_0.1.4.rds"
))
object <- updateObject(object, verbose = TRUE)
validObject(object)

hbc/bcbioRNASeq documentation built on Sept. 17, 2024, 5:47 a.m.