Uses enricher to run ORA on each of the metabolite cluster from any of the MCA functions using a pathway list
Usage
cluster_ora(
data,
metadata_info = c(ClusterColumn = "RG2_Significant", BackgroundColumn = "BG_method",
PathwayTerm = "term", PathwayFeature = "Metabolite"),
remove_background = TRUE,
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 the cluster names that ORA should be performed on (=ClusterColumn). BackgroundColumn passes the column name needed if remove_background=TRUE. Also pass ColumnName for input_pathway including term and feature names. (ClusterColumn= ColumnName data, BackgroundColumn = ColumnName data, PathwayTerm= ColumnName input_pathway, PathwayFeature= ColumnName input_pathway) c(FeatureName="Metabolite", ClusterColumn="RG2_Significant", BackgroundColumn="BG_method", PathwayTerm= "term", PathwayFeature= "Metabolite")
- remove_background
Optional: If TRUE, column BackgroundColumn name needs to be in metadata_info, which includes TRUE/FALSE for each metabolite to fall into background based on the chosen Background method for e.g. mca_2cond are removed from the universe. default: TRUE
- input_pathway
DF that must include column "term" with the pathway name, column "Feature" with the Metabolite name or ID and column "Description" with pathway description.
- pathway_name
Optional: Name of the pathway list 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