updateObject: Update a SingleCellExperiment object

In LTLA/SingleCellExperiment: S4 Classes for Single Cell Data

Update a SingleCellExperiment object

Description

Update SingleCellExperiment objects to the latest version of the class structure. This is usually called by methods in the SingleCellExperiment package rather than by users or downstream packages.

Usage

## S4 method for signature 'SingleCellExperiment'
updateObject(object, ..., verbose = FALSE)

Arguments

object	A old SingleCellExperiment object.
...	Additional arguments that are ignored.
verbose	Logical scalar indicating whether a message should be emitted as the object is updated.

Details

This function updates the SingleCellExperiment to match changes in the internal class representation. Changes are as follows:

• Objects created before 1.7.1 are modified to include altExps and reducedDims fields in their internal column metadata. Reduced dimension results previously in the reducedDims slot are transferred to the reducedDims field.

• Objects created before 1.9.1 are modified so that the size factors are stored by sizeFactors<- in colData rather than int_colData.

Value

An updated version of object.

Author(s)

Aaron Lun

See Also

objectVersion, which is used to determine if the object is up-to-date.

LTLA/SingleCellExperiment documentation built on March 28, 2024, 7:47 a.m.