buildPathway: Build a Pathway object.

In graphite: GRAPH Interaction from pathway Topological Environment

Description

This function creates a new object of type Pathway given a data frame describing its edges.

Usage

buildPathway(id, title, species, database, proteinEdges,
             metaboliteEdges = NULL, mixedEdges = NULL,
             timestamp = NULL)

Arguments

id	the pathway identifier.
title	the title of the pathway.
species	the species the pathway belongs to.
database	the name of the database the pathway derives from.
proteinEdges	a data.frame of edges between proteins (or genes). Must have the following columns: src_type, src, dest_type, dest, direction and type. Direction must be one of the two strings: "directed" or "undirected".
metaboliteEdges	interactions between metabolites. Can be NULL. Otherwise, it must have the same structure as proteinEdges.
mixedEdges	interactions between metabolites and proteins. Can be NULL. Otherwise, it must have the same structure as proteinEdges.
timestamp	when the pathway was annotated, by default the time buildPathway is called.

See Also

Pathway-class

Examples

edges <- data.frame(src_type = "ENTREZID", src="672",
                    dest_type = "ENTREZID", dest="7157",
                    direction="undirected", type="binding")
pathway <- buildPathway("#1", "example", "hsapiens", "database", edges)

# Example with metabolites:
edges <- data.frame(src_type = "ENTREZID", src="672",
                    dest_type = "ENTREZID", dest="7157",
                    direction="undirected", type="binding")
mixed <- data.frame(src_type = "CHEBI", src="77750",
                    dest_type = "ENTREZID", dest="7157",
                    direction="undirected", type="binding")
pathway <- buildPathway("#1", "example", "hsapiens", "database",
                        edges, mixedEdges = mixed)

Example output

graphite documentation built on Nov. 8, 2020, 8:12 p.m.