goTools {goTools}R Documentation

Reference GO nodes list.

Description

The function EndNodeList builds the default end node list used in ontoCompare. CustomEndNodeList helps you build a list of children nodes starting from a GO id of interest.

Usage

EndNodeList()
CustomEndNodeList(id,rank=1)

Arguments

id Valid GO id: "GO:XXXXXXX".
rank Number of levels of children of the GO DAG under id you want to add to your nodes list.

Value

EndNodeList returns a vector of all GO ids 1 level below MF("GO:0003674"), BP("GO:0008150") and CC("GO:0005575"). MF, BP and CC nodes are included. CustomEndNodeList returns a vector of all GO ids children of id, rank levels below it.

Author(s)

Yee Hwa (Jean) Yang, Agnes Paquet

See Also

ontoCompare

Examples

# Examples use the probeID dataset. For description type ? probeID.
library(GO)
library(annotate)
data(probeID)
EndNodeList()

MFendnode <- CustomEndNodeList("GO:0003674", rank=2)
ontoCompare(affylist, probeType="hgu133a", endnode=MFendnode, goType="MF")


[Package goTools version 1.0.3 Index]