ZarrRemote-class: A remote S3-like representation of Zarr folders

In Bioconductor/ZarrExperiment: Manipulate Zarr archives as R objects

A remote S3-like representation of Zarr folders

Description

The 'ZarrRemote' class allows one to display and import Zarr files on the web that are accessible via the 'S3Fs' python module <https://s3fs.readthedocs.io/en/latest/> and based on the AWS S3 service.

Usage

ZarrRemote(endpoint, bucket, resource, ...)

Arguments

endpoint	character(1) The base URL of the remote Zarr folders
bucket	character(1) The bucket name portion and any subdirectories in the full URL.
resource	character(1) Optional. A full URL typically composed of both 'endpoint' and 'bucket' components.
...	Additional inputs to the lower level class constructor

Details

The 'endpoint' component consists of both the 'scheme' and the 'domain'. The complete URL is the combination of the 'endpoint' and 'bucket' components. A complete URL can also be provided via the 'resource' argument.

Examples

zr <- ZarrRemote(
    endpoint = "https://mghp.osn.xsede.org/",
    bucket = "bir190004-bucket01/TMA11/zarr/"
)

zr <- ZarrRemote(
    resource = "https://mghp.osn.xsede.org/bir190004-bucket01/TMA11/zarr/"
)

zr

## Not run: 
  zarray <- import(zr, filename = "5.zarr")

  dim(zarray)
  ## [1] 64 3007 3007

  format(object.size(zarray), units = "GB", standard = "SI")
  ## [1] "2.3 GB"

## End(Not run)

Bioconductor/ZarrExperiment documentation built on Oct. 25, 2022, 7:41 a.m.