The DataSpaceConnection class

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

Constructor

connectDS

See also

connectDS DataSpaceR-package

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.

Examples

if (FALSE) { # \dontrun{
# 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()

} # }