Pathway-class: Class '"Pathway"'

In sales-lab/graphite: GRAPH Interaction from pathway Topological Environment

Class "Pathway"

Description

A biological pathway.

Variants

A Pathway instance actually stores multiple variants of the same biological data.

This is the list of included variants:

• proteins: includes only interactions among proteins;

• metabolites: includes only interactions among metabolites;

• mixed: includes all available interactions.

Methods

pathwayId(p):

Returns the native ID of the pathway.

pathwayTitle(p):

Returns the title of the pathway.

pathwayDatabase(p):

Returns the name of the database the pathway was derived from.

pathwaySpecies(p):

Returns the name of the species in which the pathway was annotated.

pathwayTimestamp(p):

Returns the date of pathway data retrieval.

pathwayURL(p):

Returns the URL of the pathway in its original database, if available.

convertIdentifiers(p, to):

Returns a new pathway using a different type of node identifiers.

edges(p, which = c("proteins", "metabolites", "mixed"), stringsAsFactors = TRUE):

Returns a data.frame describing the edges of this pathway.

The option which selects the desired pathway variant (see section "Variants" above).

If stringsAsFactors is TRUE, strings are converted to factors.

nodes(p, which = c("proteins", "metabolites", "mixed")):

Returns the names of the nodes belonging to this pathway.

The option which selects the desired pathway variant (see section "Variants" above).

plot(p):

Shows the pathway topology in Cytoscape.

runClipper(p, expr, classes, method, ...):

Runs a clipper analysis over the pathway.

runTopologyGSA(p, test, exp1, exp2, alpha, ...):

Runs a topologyGSA analysis over the pathway.

Author(s)

Gabriele Sales

See Also

pathways

Examples

  reactome <- pathways("hsapiens", "reactome")
  pathway <- reactome[[1]]

  pathwayTitle(pathway)
  pathwaySpecies(pathway)
  nodes(pathway)
  edges(pathway)

sales-lab/graphite documentation built on Oct. 15, 2023, 9:23 a.m.