ExcelToPloPathway {PloGO2} | R Documentation |
Function to add KEGG pathway annotation to an Excel spread sheet
ExcelToPloPathway(fname, colName = "Uniprot", compareWithReference = "none", DB.name = "pathwayDB.csv", 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 |
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 |
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" |
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") )