Function to do steps of pathway annotation and annotation/abundance plots 
Summarize pathway categories for all the files in the zip,
if provided merge data from data file,
generate annotation and abundance plots and comparison with reference.
PloPathway(zipFile = "none", reference = "none", data.file.name = "none", datafile.ignore.cols = 1, filesPath = ".", aggregateFun="sum", logAb=FALSE,...)
	Zip containing all the GO files
	The file name of the reference file, if any, for instance "Control" for Control.txt
	The file containing all the experimental data, for instance "NASF.csv"
	The number of columns in the experimental file given in data.file.name that should not be used as numerical,
		for instance 2 if there is an ID field and a Description field. By default 1.
	If the zip file is not provided, the path to the GO files
	Either "sum" or "product"; the aggregation operation for abundance data
	TRUE or FALSE; the abundance data to be logged or not
	Parameters to pass
Process all the pathway files provided, in the directory or the zip,
and assign ID's to the respective categories.  
If a reference is provided, then the numbers of identifiers in
each category is compared to the reference by means of Fisher's
exact test.  If a data file is provided, then the quantitative
values are aggregated into the sets.

A list object, with the following values:
	The GO counts matrix summarized for all files

	The GO percentages matrix summarized for all files

	The GO percentages matrix summarized for all files, ONLY generated if an
	abundance file was provided

	The aggregated abundance matrix if the data file is provided
	The Fisher p-values matrix summarized for all files, ONLY generated if
	a reference file was provided

	The full list result of processAnnotation function

	The abundance levelplots if the data.file.name is not "none"

	The abundance barcharts if the data.file.name is not "none"


J. Wu

%% ~Make other sections like Warning with \section{Warning }{....} ~

# where sample files are stored
path <- system.file("files", package = "PloGO2")
# run PloPathway with list of id's, data file and reference
res <- PloPathway( zipFile=paste(path, "PWFiles.zip", sep="/"), 
	data.file.name = paste(path, "Abundance_data.csv", sep="/"),
	datafile.ignore.cols = 1)
\keyword{ analysis }