The DataSpaceDAASH class

An R6 class for DataSpace DAASH data.

Constructor

DataSpaceConnection$getDaash()

See also

connectDS DataSpaceConnection

Super class

DataSpaceR::DataSpaceConnection -> DataSpaceDaash

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.

daashMetadata

A data.table showing the donor and mAb metadata with CDS sequence_id values for the loaded DAASH dataset.

availableStructures

A data.table showing the mAb structures available to download.

datasets

A list of DAASH datastets loaded to the DAASH object.

variableDefinitions

A data.table of variable definitions.

Methods

Public methods

• DataSpaceDaash$new()

• DataSpaceDaash$print()

• DataSpaceDaash$getFastaFromSequences()

• DataSpaceDaash$downloadAntibodyStructures()

• DataSpaceDaash$refresh()

• DataSpaceDaash$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()

---

Method new()

Initialize DataSpaceMabMetadata object. See DataSpaceConnection.

Usage

DataSpaceDaash$new(availableDaash)

Arguments

availableDaash

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

config

A list.

---

Method print()

Print the DataSpaceMab object summary.

Usage

DataSpaceDaash$print()

---

Method getFastaFromSequences()

Return a fasta file for available daash sequences that have been loaded to the current object.

Usage

DataSpaceDaash$getFastaFromSequences(
  sequenceType = "nt",
  originalHeaders = FALSE,
  path = NULL
)

Arguments

sequenceType

character the type of fasta file to return: nt = nucleotide, aa = amino acid.

originalHeaders

boolean if the original fasta headers should be provided

path

The path where to save the fasta files to. If using the default value, NULL, then a fasta file is returned as a character vector.

---

Method downloadAntibodyStructures()

Saves all antibody structures associated with the daash object's `availableStuctures` object.

Usage

DataSpaceDaash$downloadAntibodyStructures(path = tempdir(), mab_id = NULL)

Arguments

path

The directory to export fasta files to.

mab_id

A subset of mab_ids to export. If using the default, NULL, all structures in availableStuctures are downloaded.

---

Method refresh()

Refresh the DataSpaceMabMetadata object to update datasets.

Usage

DataSpaceDaash$refresh()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DataSpaceDaash$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

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

# Get the daash object using either an availableMabs or
# availableDonors object.
daash <- con$availableMabs[mab_ab_binding_type %like% "CD4"] |>
  con$getDaash()

# To get lineage sequences, query donors, then pipe available
# donors to the connection getDaash object.
daash <- con$availableDonors[
  lineage_sequences_available == TRUE & mab_count < 10,
  ] |>
  con$getDaash()

# Inspect what datasets are available
names(daash$datasets)

# Inspect the `topCalls` dataset
daash$datasets$topCalls

} # }