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Update object

Usage

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

# S4 method for 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.

Value

Modified object.

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.

Note

Updated 2022-05-07.

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.

Author

Michael Steinbaugh

Examples

data(bcb)

## bcbioRNASeq ====
object <- bcb
object <- updateObject(object)
validObject(object)
#> [1] TRUE

## Example that depends on remote file.
object <- pipette::import(file = file.path(
    bcbioRNASeqTestsURL,
    "bcbioRNASeq_0.1.4.rds"
))
#> → Downloading <http://r.acidgenomics.com/testdata/bcbiornaseq/v0.5/bcbioRNASeq_0.1.4.rds> to /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpnjSttX/pipette-7a353a8f05e3.rds.
#> → Importing <http://r.acidgenomics.com/testdata/bcbiornaseq/v0.5/bcbioRNASeq_0.1.4.rds> using base::`readRDS()`.
object <- updateObject(object, verbose = TRUE)
#> 
#> 🧪 # Update object
#> → Updating `bcbioRNASeq` object from version "0.1.4" to "0.5.0".
#> 🧪 ## Legacy slots
#>  `NAMES` slot must be set to "NULL".
#>  `elementMetadata` slot must contain a zero-column `DataFrame`.
#> ! Slotting empty `rowRanges()`.
#> ! Dropping legacy `bcbio` slot.
#> 🧪 ## Metadata
#> ! Setting `bcbioLog` as "empty character".
#> ! Setting `bcbioCommands` as "empty character".
#> ! Stashing empty `call`.
#> ! Setting `caller` as "salmon".
#> ! Dropping legacy `design`.
#> → Renaming `ensemblVersion` to `ensemblRelease`.
#> → Setting `ensemblRelease` as "integer".
#> → Setting `gffFile` as "empty character".
#> → Setting `lanes` as integer.
#> → Setting `level` as "genes".
#> → Renaming `programs` to `programVersions`.
#> → Coercing `programVersions` to `DataFrame`.
#> → Setting `sampleMetadataFile` as "empty character".
#> → Simplifying stashed `sessionInfo`.
#> → Dropping legacy `template`.
#> ! Dropping `unannotatedGenes` from `metadata()`.
#> 🧪 ### tximport
#> ! Setting `countsFromAbundance` as "lengthScaledTPM".
#> → Coercing `tx2gene` to `Tx2Gene` class object.
#> 🧪 ## Assays
#> → Coercing `vst` assay from "DESeqTransform" to "matrix".
#> → Coercing `rlog` assay from "DESeqTransform" to "matrix".
#> → Renaming `raw` assay to `counts`.
#> → Dropping `tmm` from `assays()`. Calculating on the fly instead.
#> 🧪 ## Row ranges
#> 🧪 ## Column data
#> → Moving `metrics` from `metadata()` into `colData()`.
#> → Renaming `x53Bias` to `x5x3Bias`.
#>  Update of `bcbioRNASeq` object was successful.
#> [updateObject] Validating the updated object ... 
#> OK
validObject(object)
#> [1] TRUE