goTools {goTools} | R Documentation |
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, 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. |
objM |
results from ontoCompare. |
... |
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)