ExcelToPloPathway: Function to add KEGG pathway annotation to an Excel spread...

In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

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") )

PloGO2 documentation built on Nov. 8, 2020, 5:40 p.m.