updateAnnotation: Update cell type annotation

In massonix/HCATonsilData: Provide programmatic access to the tonsil cell atlas datasets

Update cell type annotation

Description

Annotations are dynamic by nature. As more experts look into the data and newer literature comes out, we expect annotations to be refined over time. We have accommodated this by allowing us and users to add new annotations to the SingleCellExperiment objects. If you want to propose a new annotation based on your experience or new evidence, please open an issue at https://github.com/massonix/HCATonsilData/issues.

Usage

updateAnnotation(sce, refAnnotation = "20220215", newAnnotation = "20220619")

Arguments

sce	A SingleCellExperiment object obtained using HCATonsilData function.
refAnnotation	string specifying the date of the annotation to use as reference.
newAnnotation	string specifying the suffix to add to the new column (annotation_*).

Value

A SingleCellExperiment object with additional an additional column (annotation_*) that contains more annotations.

Examples

# update the annotation from preprint (version 1.0) to publication (version 2.0)
## Not run: 
sce <- updateAnnotation(
  sce,
  refAnnotation = "20220619",
  newAnnotation = "20230508"
)

## End(Not run)

massonix/HCATonsilData documentation built on May 7, 2024, 8:33 a.m.