makeGOGraph {GOstats} | R Documentation

## Construct a GO Graph

### Description

The directed acyclic graph (DAG) based on finding the most specific terms for the supplied identifiers is constructed and returned. The constructuion is per GO ontology (there are three, MF, BP and CC) and once the most specific terms have been identified then all less specific terms are found (these are the parents of the terms) and then their parents and so on, until the root is encountered.

### Usage

    makeGOGraph(x, what="MF", lib="hgu95av2", removeRoot = TRUE)

### Arguments

`x` | A vector of identifiers.
`what` | Which of the GO ontologies to use.
`lib` | The name of a meta-data package to use for mapping the identifiers to GO identifiers.
`removeRoot` | A logical value indicating whether the GO root nood should be removed or not.

### Details

The mapping of manufacturers identifiers (e.g. Affymetrix) to GO identifiers is done on the basis of an initial mapping to LocusLink identifiers. For many data sources these are available from the Bioconductor Project (www.bioconductor.org).

Once that mapping has occurred we obtain from the meta-data package the mapping to the most specific terms (again these have been precomputed) and using those together with the GO package (again from Bioconductor) mapping to all parents down to the root node is performed.

The mappings are different for the different ontologies. Typically a GO indentifier is used only in one specific ontology.

The resulting structure is stored in a graph using the `graph` package, again from Bioconductor.

### Value

An object that inherits from the `graph` class. The particular implementation is not specified.

### Author(s)

R. Gentleman

### References

The Gene Ontology Consortium

### See Also

`oneGOGraph`

### Examples

     gN <- c("38940_at","2073_s_at", "35580_at",  "34701_at")
     gg1 <- makeGOGraph(gN, "BP", "hgu95av2")

[Package Contents]