Pathway-class {graphite} | R Documentation

## 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`

[Package graphite version 1.26.3 Index]