Uses enricher to run ORA on the differential metabolites (DM) using a pathway list

Usage

standard_ora(
  data,
  metadata_info = c(pvalColumn = "p.adj", percentageColumn = "t.val", PathwayTerm =
    "term", PathwayFeature = "Metabolite"),
  cutoff_stat = 0.05,
  cutoff_percentage = 10,
  input_pathway,
  pathway_name = "",
  min_gssize = 10,
  max_gssize = 1000,
  save_table = "csv",
  path = NULL
)

Arguments

data: DF with metabolite names/metabolite IDs as row names. Metabolite names/IDs need to match the identifier type (e.g. HMDB IDs) in the input_pathway.
metadata_info: Optional: Pass ColumnName of the column including parameters to use for cutoff_stat and cutoff_percentage. Also pass ColumnName for input_pathway including term and feature names. (pvalColumn = ColumnName data, percentageColumn= ColumnName data, PathwayTerm= ColumnName input_pathway, PathwayFeature= ColumnName input_pathway) c(pvalColumn="p.adj", percentageColumn="t.val", PathwayTerm= "term", PathwayFeature= "Metabolite")
cutoff_stat: Optional: p-adjusted value cutoff from ORA results. Must be a numeric value. default: 0.05
cutoff_percentage: Optional: percentage cutoff of metabolites that should be considered for ORA. Selects top/Bottom % of selected percentageColumn, usually t.val or Log2FC default: 10
input_pathway: 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.
pathway_name: Optional: Name of the input_pathway used default: ""
min_gssize: Optional: minimum group size in ORA default: 10
max_gssize: Optional: maximum group size in ORA default: 1000
save_table: Optional: File types for the analysis results are: "csv", "xlsx", "txt" default: "csv"
path: Optional: Path to the folder the results should be saved at. default: NULL

Value

Saves results as individual .csv files.