PloGO: Function to do steps of GO annotation and...
In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

Description Usage Arguments Details Value Author(s) See Also Examples

Summarize GO categories for all the files in the zip, if provided merge data from data file, generate annotation and abundance plots and comparison with reference.

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PloGO(zipFile = "none", termFile="none", ontology = "BP", ontologyLevel = 2, reference = "none", data.file.name = "none", datafile.ignore.cols = 1, 
		filesPath=".", node=NULL, aggregateFun="sum", logAb=FALSE, ...)

`zipFile`	Zip containing all the GO files
`termFile`	A file with the GO terms of interest, if a limited set provided
`ontology`	Wither BP, MF or CC
`ontologyLevel`	A small level such as 2 or 3
`reference`	The file name of the reference file, if any, for instance "Control" for Control.txt
`data.file.name`	The file containing all the experimental data, for instance "NASF.csv"
`datafile.ignore.cols`	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.
`filesPath`	If the zip file is not provided, the path to the GO files
`node`	NULL, ignored at the moment
`aggregateFun`	Either "sum" or "product"; the aggregation operation for abundance data
`logAb`	TRUE or FALSE; the abundance data to be logged or not
`...`	Parameters to pass

Process all the GO files provided, in the directory or the zip, and assign ID's to the respective categories. The categories can come from a target list, or from a choice of level and ontology. 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:

`Counts`	The GO counts matrix summarized for all files
`Percentages`	The GO percentages matrix summarized for all files
`Abundance`	The GO percentages matrix summarized for all files, ONLY generated if an abundance file was provided
`aggregatedAbundance`	The aggregated abundance matrix if the data file is provided
`FisherPval`	The Fisher p-values matrix summarized for all files, ONLY generated if a reference file was provided
`res.list`	The full list result of processAnnotation function
`list.levelplots`	The abundance levelplots if the data.file.name is not "none"
`list.barplots`	The abundance barcharts if the data.file.name is not "none"

D. Pascovici

processAnnotation

# where sample files are stored
path <- system.file("files", package = "PloGO2")
# run PloGO with list of id's, data file and reference
res <- PloGO( zipFile=paste(path, "GOfiles.zip", sep="/"), 
	reference="Control", termFile = paste(path, "GOListDrought.txt", sep="/"),
	data.file.name = paste(path, "NSAFDesc.csv", sep="/"),
	datafile.ignore.cols = 2)