ontoCompare: Wrapper functions
In goTools: Functions for Gene Ontology database

Description Usage Arguments Value Author(s) Examples

View source: R/goTools.R

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

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

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

`genelist`	list of 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.Valid probe types include GO ids and any probes ids for which a BioC annotation package providing a mapping to GO is available. 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.
`beside`	Logical. If 'TRUE', the bars of the barplot are portrayed as juxtaposed bars. See ?barplot for more details.
`las`	numeric: if las=2, the axis labels are displayed perpendicular to the axis. See ?par for more details.
`legend.text`	vector of text used to construct a legend for the plot. See ?barplot for more details.
`objM`	results from ontoCompare.
`names.arg`	Labels to use in ontoPlot.
`...`	extra layout parameters to be passed to ontoPlot.

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

Yee Hwa (Jean) Yang, Agnes Paquet

# Examples use the probeID dataset. For description type ?probeID.
# Not run

#library(GO.db)
#data(probeID)
#ontoCompare(affylist, probeType="hgu133a", plot=TRUE)
#res <- ontoCompare(operonlist["L1"], probeType="operon", method="TIDS")
#ontoPlot(res, cex=0.7)