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
SaveAs_Table: Optional: File types for the analysis results are: "csv", "xlsx", "txt" default: "csv"
FolderPath: Optional: Path to the folder the results should be saved at. default: NULL

Value

Saves results as individual .csv files.