The DataSpaceMab class

An R6 class for DataSpace MAb data.

Constructor

DataSpaceConnection$getMab()

See also

connectDS DataSpaceConnection

Super class

DataSpaceR::DataSpaceConnection -> DataSpaceMabs

Active bindings

mabMetadata

A data.table of mAbs with metadata found in the object.

donorMetadata

A data.table of donors with metadata found in the object.

mabMixMetadata

A data.table. A table of mAb mixtures with metadata found in this DataSpaceMab instance.

mabMix

A data.table. A mapping table of mab_mix_id to mab_id. with metadata found in this DataSpaceMab instance.

datasets

A list of data.table objects containing the mab related that were loaded.

variableDefinitions

A data.table of variable definitions.

Methods

Public methods

• DataSpaceMabs$new()

• DataSpaceMabs$print()

• DataSpaceMabs$loadDaash()

• DataSpaceMabs$refresh()

• DataSpaceMabs$clone()

Inherited methods

• DataSpaceR::DataSpaceConnection$downloadPublicationData()
• DataSpaceR::DataSpaceConnection$filterMabGrid()
• DataSpaceR::DataSpaceConnection$getDaash()
• DataSpaceR::DataSpaceConnection$getDonors()
• DataSpaceR::DataSpaceConnection$getGroup()
• DataSpaceR::DataSpaceConnection$getGroups()
• DataSpaceR::DataSpaceConnection$getMab()
• DataSpaceR::DataSpaceConnection$getMabs()
• DataSpaceR::DataSpaceConnection$getStudies()
• DataSpaceR::DataSpaceConnection$getStudy()
• DataSpaceR::DataSpaceConnection$resetMabGrid()

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Method new()

Initialize DataSpaceMab object. See DataSpaceConnection.

Usage

DataSpaceMabs$new(mabIds, includeMixtures)

Arguments

mabIds

A character vector of `mab_id` values.

includeMixtures

Whether or not to include mab mixtures. "yes", "no", or "only" are valid.

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Method print()

Print the DataSpaceMab object summary.

Usage

DataSpaceMabs$print()

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Method loadDaash()

Load any available DAASH datasets.

Usage

DataSpaceMabs$loadDaash()

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Method refresh()

Refresh the DataSpaceMab object to update datasets.

Usage

DataSpaceMabs$refresh()

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Method clone()

The objects of this class are cloneable with this method.

Usage

DataSpaceMabs$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{
# Create a connection (Initiate a DataSpaceConnection object)
con <- connectDS()

# Inspect available mabs, then pass subset to the `getMabs` method.
vrc01 <- con$availableMabs[mab_name_std == "VRC01"] |>
  con$getMabs()

# Inspect the `NABMAb` assay data.
vrc01$datasets$NABMAb

# Load DAASH data from mab object
vrc01$loadDaash()

# Inspect DAASH datasets
vrc01$datasets$daash |> names()

} # }