makeGOGraph: Construct a GO Graph

Description

The directed acyclic graph (DAG) based on finding the most specific terms for the supplied Entrez Gene IDs 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, Ontology = "MF", removeRoot = TRUE, mapfun = NULL, chip = NULL)

Arguments

A vector of Entrez Gene IDs.

Ontology

Which GO ontology to use (CC, BP, or MF).

removeRoot

A logical value indicating whether the GO root node should be removed or not.

mapfun

A function taking a character vector of Entrez Gene IDs as its only argument and returning a list of "GO lists" matching the structure of the lists in the GO maps of annotation data packages. The function should behave similarly to mget(x, eg2gomap, ifnotfound=NA), that is, NA should be returned if a specified Entrez ID has no GO mapping. See details for the interaction of mapfun and chip.

chip

The name of a DB-based annotation data package (the name will end in ".db"). This package will be used to generate an Entrez ID to GO ID mapping instead of mapfun.

Value

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

Details

For each supplied Entrez Gene identifier all the GO annotations (in the specified ontology) are found. The mapping is achieved in one of three ways:

If mapfun is provided, it will be used to perform the needed lookups. In this case, chip will be ignored.

If chip is provided and mapfun=NULL, then the needed lookups will be done based on the Entrez to GO mappings encapsulated in the specified annotation data package. This is the recommended usage.

If mapfun and chip are NULL or missing, then the function will attempt to load the GO package (the environment-based package, distinct from GO.db). This package contains a legacy environment mapping Entrez IDs to GO IDs. If the GO package is not available, an error will be raised. Omitting both mapfun and chip is not recommended as it is not compatible with the DB-based annotation data packages.

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.

References

The Gene Ontology Consortium

Examples

Run this code

 library("hgu95av2.db")
 set.seed(321)
 gN <- unique(sample(keys(hgu95av2.db, 'ENTREZID'), 4))
 gg1 <- makeGOGraph(gN, "BP", chip="hgu95av2.db")

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