ExcelToPloGO {PloGO2} | R Documentation

## Function to add GO annotation to an Excel spread sheet

### Description

Function to add GO annotation to an Excel spread sheet

### Usage

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

### Arguments

`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

### Value

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"

### Author(s)

D.Pascovici

### Examples

    ## 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)

[Package PloGO2 version 1.4.0 Index]