Usage
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, ...)
Arguments
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.