Reduce mapping ambiguities by using detected IDs

Usage

CleanMapping(
  InputData,
  PriorKnowledge,
  DetectedID = "HMDB",
  GroupingVariable = "term",
  From = "MetaboliteID",
  To = "hmdb",
  SaveAs_Table = "csv",
  FolderPath = NULL
)

Arguments

InputData: Dataframe with at least one column with the target (e.g. metabolite)
PriorKnowledge: Dataframe with at least one column with the "original target metabolite ID", "source" (e.g. term) and the "translated target metabolite ID".
SettingsInfo

Value

Prior Knowledge usable for enrichment analysis

Examples

DetectedIDs <-  MetaProViz::ToyData(Data="Cells_MetaData")%>% rownames_to_column("Metabolite") %>%select("Metabolite", "HMDB")
#> Error in MetaProViz::ToyData(Data = "Cells_MetaData") %>% rownames_to_column("Metabolite") %>%     select("Metabolite", "HMDB"): could not find function "%>%"
PathwayFile <- MetaProViz::TranslateID(InputData= MetaProViz::LoadKEGG(), SettingsInfo = c(InputID="MetaboliteID", GroupingVariable="term"), From = c("kegg"), To = c("hmdb"))[["TranslatedDF"]]
#> Installing package into ‘/home/runner/work/_temp/Library’
#> (as ‘lib’ is unspecified)
#> also installing the dependencies ‘gargle’, ‘uuid’, ‘ids’, ‘rematch2’, ‘conflicted’, ‘dbplyr’, ‘dtplyr’, ‘googledrive’, ‘googlesheets4’, ‘haven’, ‘reprex’
#> `Error in .getUrl(url, .flatFileParser) : Not Found (HTTP 404).` for pathway hsa01524 - Skipping and continuing to the next query.
#> `Error in .getUrl(url, .flatFileParser) : Not Found (HTTP 404).` for pathway hsa01523 - Skipping and continuing to the next query.
#> `Error in .getUrl(url, .flatFileParser) : Not Found (HTTP 404).` for pathway hsa01522 - Skipping and continuing to the next query.
Res <- MetaProViz::CleanMapping(InputData= DetectedIDs, PriorKnowledge= PathwayFile, DetectedID="HMDB", GroupingVariable="term", From="MetaboliteID", To="hmdb")