buildPathway {graphite} | R Documentation

## Build a Pathway object.

### 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)

[Package graphite version 1.26.3 Index]