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Gene Walk Network Generator

GeneWalkGenerator.Rd

R6 class to build Gene Walk networks from internal database sources. Supports building a master network once and subsetting to multiple gene sets.

Public fields

pathway_sources

Character vector of pathway sources

pathway_namespaces

List of namespace filters per pathway source

ppi_sources

Character vector of PPI sources

ppi_params

List of PPI filtering parameters

Methods

Public methods

Method new()

Initialise the generator

Usage

GeneWalkGenerator$new()

Method print()

Print for GeneWalkGenerator

Usage

GeneWalkGenerator$print(...)

Arguments

...

Additional parameters to forward to the print

Method add_pathways()

Add pathway sources to the network

Usage

GeneWalkGenerator$add_pathways(
  source = c("go", "reactome"),
  go_namespace = c("biological_process", "molecular_function", "cellular_component")
)

Arguments

source

Character vector of sources: "go", "reactome". Defaults to "go" only by default.

go_namespace

Character vector. Specifically for GO. Choices are c("biological_process", "molecular_function", "cellular_component")

Method add_ppi()

Add PPI sources to the network

Usage

GeneWalkGenerator$add_ppi(
  source = c("combined", "string", "signor", "reactome", "intact"),
  string_threshold = NULL,
  intact_threshold = NULL,
  intact_physical_only = FALSE
)

Arguments

source

Character vector of sources

string_threshold

Numeric threshold for STRING scores

intact_threshold

Numeric threshold for Intact scores

intact_physical_only

Logical, only physical interactions from Intact

Method build()

Build the full network from selected sources

Usage

GeneWalkGenerator$build(.verbose = TRUE)

Arguments

.verbose

Boolean. Controls the verbosity of the function

Method create_for_genes()

Create a gene-specific GeneWalk object

Usage

GeneWalkGenerator$create_for_genes(genes)

Arguments

genes

Character vector of gene symbols

Returns

Returns the initialised GeneWalk.

Method reset_choices()

Resets the internal choices and erases any stored network data.

Usage

GeneWalkGenerator$reset_choices()

Method return_full_network_dt()

Returns the full network data.table.

Usage

GeneWalkGenerator$return_full_network_dt()

Returns

data.table with the full internal network.

Method clone()

The objects of this class are cloneable with this method.

Usage

GeneWalkGenerator$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.