ExcelToPloPathway {PloGO2} | R Documentation

## Function to add KEGG pathway annotation to an Excel spread sheet

### Description

Function to add KEGG pathway annotation to an Excel spread sheet

### Usage

    ExcelToPloPathway(fname, colName = "Uniprot", compareWithReference = "none", DB.name = "pathwayDB.csv", 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
`compareWithReference` | The name of the tab that serves as basis for enrichment comparison.
`DB.name` | The DB file name for the pathway
`data.file.name` | Abundance data for PloGO if any
`outFolder` | The output files folder

### Value

A list object, with the following values:

`Counts` | The pathway counts matrix summarized for all files
`Percentages` | The pathway percentages matrix summarized for all files
`Abundance` | The pathway percentages matrix summarized for all files, ONLY generated if an abundance file was provided
`aggAbundance` | Aggregated abundance matrix by combination of tab and abundance file columns for all pathways
`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"

### Examples

    path <- system.file("files", package = "PloGO2")

    res <- ExcelToPloPathway(file.path(path, "ResultsWGCNA_Input4PloGO2.xlsx"),
    	colName="Uniprot", compareWithReference="AllData", DB.name=file.path(path, "pathwayDB.csv"),
    	data.file.name = file.path(path, "Abundance_data.csv") )

[Package PloGO2 version 1.6.0 Index]