Uses enricher to run ORA on the differential metabolites (DM) using a pathway list
Usage
StandardORA(
InputData,
SettingsInfo = c(pvalColumn = "p.adj", PercentageColumn = "t.val", PathwayTerm =
"term", PathwayFeature = "Metabolite"),
pCutoff = 0.05,
PercentageCutoff = 10,
PathwayFile,
PathwayName = "",
minGSSize = 10,
maxGSSize = 1000,
SaveAs_Table = "csv",
FolderPath = NULL
)Arguments
- InputData
DF with metabolite names/metabolite IDs as row names. Metabolite names/IDs need to match the identifier type (e.g. HMDB IDs) in the PathwayFile.
- SettingsInfo
Optional: Pass ColumnName of the column including parameters to use for pCutoff and PercentageCutoff. Also pass ColumnName for PathwayFile including term and feature names. (pvalColumn = ColumnName InputData, PercentageColumn= ColumnName InputData, PathwayTerm= ColumnName PathwayFile, PathwayFeature= ColumnName PathwayFile) c(pvalColumn="p.adj", PercentageColumn="t.val", PathwayTerm= "term", PathwayFeature= "Metabolite")
- pCutoff
Optional: p-adjusted value cutoff from ORA results. Must be a numeric value. default: 0.05
- PercentageCutoff
Optional: Percentage cutoff of metabolites that should be considered for ORA. Selects Top/Bottom % of selected PercentageColumn, usually t.val or Log2FC default: 10
- PathwayFile
DF that must include column "term" with the pathway name, column "Metabolite" with the Metabolite name or ID and column "Description" with pathway description that will be depicted on the plots.
- PathwayName
Optional: Name of the PathwayFile used default: ""
- minGSSize
Optional: minimum group size in ORA default: 10
- maxGSSize
Optional: maximum group size in ORA default: 1000
- FolderPath
Optional: Path to the folder the results should be saved at. default: NULL
- Save_as_Results
Optional: File types for the analysis results are: "csv", "xlsx", "txt" default: "csv"