DataSpaceConnection: The DataSpaceConnection class

In DataSpaceR: Interface to 'the CAVD DataSpace'

The DataSpaceConnection class

Description

An R6 class for DataSpace browsing and fetching data in DataSpace.

Constructor

connectDS

Active bindings

config

A list. Stores configuration of the connection object such as URL, path and username.

availableStudies

A data.tabl of available studies.

availableGroups

A data.table of available groups.

availableMabs

A data.table of available mAbs.

availableMabMixtures

A data.table. Metadata of available mAb mixtures.

availableDonors

A data.table. Metadata about all mAb donors in the DataSpace.

availableViruses

A data.table of metadata about all virsues in the DataSpace and virus name synonyms.

availablePublications

A data.table of available publications metadata and available datasets.

lanlMabMetadata

A data.table of mAb metadata from LANL of mAbs found in the object

virusNameMappingTables

A list of data.tables containing virus name mappings.

mabGridSummary

Defunct. Use 'availableMabs'.

mabGrid

Defunct. Use 'availableMabs'.

virusMetadata

Defunct. Use 'virusNameMappingTables'.

Methods

Public methods

• DataSpaceConnection$new()

• DataSpaceConnection$print()

• DataSpaceConnection$getStudies()

• DataSpaceConnection$getGroups()

• DataSpaceConnection$getMabs()

• DataSpaceConnection$getDonors()

• DataSpaceConnection$getDaash()

• DataSpaceConnection$downloadPublicationData()

• DataSpaceConnection$loadLanlMabMetadata()

• DataSpaceConnection$getStudy()

• DataSpaceConnection$getGroup()

• DataSpaceConnection$getMab()

• DataSpaceConnection$filterMabGrid()

• DataSpaceConnection$resetMabGrid()

• DataSpaceConnection$refresh()

• DataSpaceConnection$clone()

---

DataSpaceConnection$new()

Initialize a DataSpaceConnection object. See connectDS.

Usage

DataSpaceConnection$new(
  login = NULL,
  password = NULL,
  verbose = FALSE,
  onStaging = FALSE
)

Arguments

login

A character. Optional argument. If there is no netrc file a temporary one can be written by passing login and password of an active DataSpace account.

password

A character. Optional. The password for the selected login.

verbose

A logical. Whether to print the extra details for troubleshooting.

onStaging

A logical. Whether to connect to the staging server instead of the production server.

Returns

A new 'DataSpaceConnection' object.

---

DataSpaceConnection$print()

Print the DataSpaceConnection object.

Usage

DataSpaceConnection$print()

---

DataSpaceConnection$getStudies()

Create a 'DataSpaceStudies' object.

Usage

DataSpaceConnection$getStudies(availableStudies = self$availableStudies)

Arguments

availableStudies

an 'availableStudies' object, or a vector of 'study_id' values.

---

DataSpaceConnection$getGroups()

Create a 'DataSpaceGroups' object.

Usage

DataSpaceConnection$getGroups(availableGroups = self$availableGroups)

Arguments

availableGroups

an 'availableGroups' object, or a vector of 'group id' values.

---

DataSpaceConnection$getMabs()

Create a 'DataSpaceMabs' object.

Usage

DataSpaceConnection$getMabs(
  availableMabs = self$availableMabs,
  includeMixtures = "yes"
)

Arguments

availableMabs

an 'availableMabs' or 'availableMabMixtures' object, or a vector of 'mab id' values. 'mab_id' values are inferred from 'availableMabMixtures' objects.

includeMixtures

Whether or not to include mab mixtures. "yes", "no", or "only" are valid. The default, "yes", will return any available mAb mixtures for any mAb passed here.

---

DataSpaceConnection$getDonors()

Create a 'DataSpaceDonors' object.

Usage

DataSpaceConnection$getDonors(availableDonors = self$availableDonors)

Arguments

availableDonors

an 'availableDonors' object, or a vector of 'donor_id' values.

---

DataSpaceConnection$getDaash()

Create a 'DataSpaceDaash' object.

Usage

DataSpaceConnection$getDaash(availableDaash = NULL)

Arguments

availableDaash

an 'availableMabs', or 'availableDonors' object, or a vector of 'sequnce_id' values.

---

DataSpaceConnection$downloadPublicationData()

Download study related publication datasets.

Usage

DataSpaceConnection$downloadPublicationData(
  availablePublications = NULL,
  downloadDir = tempdir()
)

Arguments

availablePublications

an 'availablePublications' object or a vector of 'publication_id' values.

downloadDir

A character. Optional, specifies directory to download nonstandard datasets. Default is use to the R session temp directory

---

DataSpaceConnection$loadLanlMabMetadata()

Load any available mAb metadata from LANL.

Usage

DataSpaceConnection$loadLanlMabMetadata()

---

DataSpaceConnection$getStudy()

Defunct. Use 'getStudies'.

Usage

DataSpaceConnection$getStudy()

---

DataSpaceConnection$getGroup()

Defunct. Use 'getGroups'.

Usage

DataSpaceConnection$getGroup()

---

DataSpaceConnection$getMab()

Defunct. Use 'getMabs'.

Usage

DataSpaceConnection$getMab()

---

DataSpaceConnection$filterMabGrid()

Defunct. Use 'availableMabs'.

Usage

DataSpaceConnection$filterMabGrid()

---

DataSpaceConnection$resetMabGrid()

Defunct. Use 'availableMabs'.

Usage

DataSpaceConnection$resetMabGrid()

---

DataSpaceConnection$refresh()

Refresh the connection object to update available studies and groups.

Usage

DataSpaceConnection$refresh()

---

DataSpaceConnection$clone()

The objects of this class are cloneable with this method.

Usage

DataSpaceConnection$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

connectDS DataSpaceR-package

Examples

## Not run: 
# Create a connection (Initiate a DataSpaceConnection object)
con <- connectDS()

# View available data

con$availableStudies
con$availableGroups
con$availablePublications
con$availableMabs
con$availableMabMixtures
con$availableDonors
con$availableViruses

# Pass an available object to a "get" method to get data

cvd408 <- con$availableStudies[study_id == "cvd408"] |>
  con$getStudies()

cd4Mabs <- con$availableMabs[grepl("CD4bs", mab_ab_binding_type)] |>
  con$getMabs()


## End(Not run)

DataSpaceR documentation built on Aug. 27, 2026, 1:06 a.m.