optimus_loom_annotation: HCA loom file annotation

View source: R/optimus_loom_annotation.R

optimus_loom_annotationR Documentation

HCA loom file annotation

Description

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.

Usage

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)

Arguments

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 LoomExperiment::import().

catalog

character() HCA catalog from which the .loom file originated.

Value

A 'LoomExperiment' object annotated with additional metadata() and colData() derived from the manifest file describing samples in the object.

See Also

manifest() and related functions for working with data returned from the */manifest/* HCA API endpoints.


Bioconductor/hca documentation built on July 28, 2022, 6:04 p.m.