optimus_loom_annotation {hca} | R Documentation |
optimus_loom_annotation()
takes the file path
location of a .loom file generated by the Optimus pipeline, for
which additional data will be extracted from the appropriate
manifest. The .loom file will be imported as a LoomExperiment
object, and the additional manifest information will be added
to the object for return.
optimus_loom_annotation(loom, catalog = NULL) ## S3 method for class 'character' optimus_loom_annotation(loom, catalog = NULL) ## S3 method for class 'LoomExperiment' optimus_loom_annotation(loom, catalog = NULL)
loom |
Either a character(1) file path to a loom file on
user's system, or a loom file obtained from the HCA and
imported into R using |
catalog |
character() HCA catalog from which the .loom file originated. |
A 'LoomExperiment' object annotated with additional
metadata()
and colData()
derived from the manifest file
describing samples in the object.
manifest()
and related functions for working with data
returned from the */manifest/*
HCA API endpoints.