buildPathway {graphite} | R Documentation |
This function creates a new object of type Pathway
given a data
frame describing its edges.
buildPathway(id, title, species, database, proteinEdges, metaboliteEdges = NULL, mixedEdges = NULL, timestamp = NULL)
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 |
mixedEdges |
interactions between metabolites and proteins. Can be |
timestamp |
when the pathway was annotated, by default the time
|
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)