goTools {goTools}R Documentation

Wrapper functions

Description

This functions will allow you to describe and compare sets of oligo ids using Gene Ontology database

Usage


ontoCompare(obj,  method=c("TGenes", "TIDS", "none"),
            probeType=c("GO", "operon", "hgu133a"), goType="All",
            plot=FALSE,endnode, ...)

ontoPlot(objM, beside=TRUE, las=2,legend.text=TRUE, ...)

Arguments

obj list of valid probe ids.
method method used to evaluate the percentage of oligos for each end-node. 'TGenes' = for each end node, return the number of direct children found / total number of probe ids. (default). This includes oligos which do not have GO annotations. 'TIDS' = for each end node, return the number of direct children found / total number of GO ids describing the list. 'none' = for each end node, return the number of direct children found.
probeType type of input given to the function. ontoCompare is expecting valid probe ids.
goType help sort the data by type. If 'All' (default), all oligos are taken into account. 'BP' restricts information to Biological Process, 'CC' to Cellular Component, and 'MF' to Molecular Function.
plot logical: if 'TRUE', results are output as a graph.
endnode list of GO ids corresponding to end-nodes of interest.
objM result from ontoCompare.
... extra layout parameters to be passed to ontoPlot.

Value

Returns the percentage of probes children of nodes contained in endnode. If 'plot' = TRUE, results are plotted as a pie chart or a bargraph.

Author(s)

Yee Hwa (Jean) Yang, Agnes Paquet

Examples

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

ontoCompare(affylist, probeType="hgu133a", plot=TRUE)
res <- ontoCompare(operonlist["L1"], probeType="operon", method="TIDS")
ontoPlot(res, cex=0.7)

[Package goTools version 1.0.3 Index]