oneGOGraph: Construct the GO graph given a set of leaves.

In Bioconductor/GOstats: Tools for manipulating GO and microarrays

Construct the GO graph given a set of leaves.

Description

Given one or more GO identifiers (which indicate the leaves in the graph) and a set of mappings to the less specific sets of nodes this function will construct the graph that includes that node and all children down to the root node for the ontology.

Usage

oneGOGraph(x, dataenv)
GOGraph(x, dataenv)

Arguments

x	A character vector of GO identifiers.
dataenv	An environment for finding the parents of that term.

Details

For any set of GO identifiers (from a common ontology) we define the induced GO graph to be that graph, based on the DAG structure (child - parent) of the GO ontology of terms, which takes the most specific set of GO terms that apply (for that ontology) and then joins these to all less specific terms. These functions help construct such graphs.

Value

The induced GO graph (or NULL) for the given GO identifier.

Author(s)

R. Gentleman

See Also

makeGOGraph

Examples

 library("GO.db")
 g1 <- oneGOGraph("GO:0003680", GOMFPARENTS)
 g2 <- oneGOGraph("GO:0003701", GOMFPARENTS)
 g3 <- join(g1, g2)

 g4 <- GOGraph(c("GO:0003680", "GO:0003701"), GOMFPARENTS)
if( require("Rgraphviz") && interactive() )
  plot(g3)

Bioconductor/GOstats documentation built on Nov. 2, 2024, 6:34 a.m.