ExcelToPloGO: Function to add GO annotation to an Excel spread sheet
In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

Description Usage Arguments Value Author(s) Examples

Function to add GO annotation to an Excel spread sheet

1	ExcelToPloGO(fname, colName = "Uniprot", termFile= NA, compareWithReference="none", data.file.name = "none", outFolder = "PloGO2Output")

`fname`	Name of the Excel spread sheet to be annotated
`colName`	The name of the column containing the protein identifiers
`termFile`	The name of the file containing the GO categories
`compareWithReference`	The name of the tab that serves as basis for enrichement comparison.
`data.file.name`	Abundance data for PloGO if any
`outFolder`	The output files folder

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
`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

## Not run: 
# where sample files are stored
path <- system.file("files", package = "PloGO2")
termFile = paste(path, "GODefault.txt", sep="/")
xlfile <- paste(path, "ResultsWGCNA_Input4PloGO2.xlsx", sep="/")

res <- ExcelToPloGO(xlfile, termFile=termFile, compareWithReference="AllData")



## End(Not run)