This script allows you ClusterORA
Usage
ClusterORA(
InputData,
SettingsInfo = c(ClusterColumn = "RG2_Significant", BackgroundColumn = "BG_Method",
PathwayTerm = "term", PathwayFeature = "Metabolite"),
RemoveBackground = TRUE,
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 the cluster names that ORA should be performed on (=ClusterColumn). BackgroundColumn passes the column name needed if RemoveBackground=TRUE. Also pass ColumnName for PathwayFile including term and feature names. (ClusterColumn= ColumnName InputData, BackgroundColumn = ColumnName InputData, PathwayTerm= ColumnName PathwayFile, PathwayFeature= ColumnName PathwayFile) c(FeatureName="Metabolite", ClusterColumn="RG2_Significant", BackgroundColumn="BG_Method", PathwayTerm= "term", PathwayFeature= "Metabolite")
- RemoveBackground
Optional: If TRUE, column BackgroundColumn name needs to be in SettingsInfo, 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
- PathwayFile
DF that must include column "term" with the pathway name, column "Feature" with the Metabolite name or ID and column "Description" with pathway description.
- PathwayName
Optional: Name of the pathway list 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