inst/examples/fileMDB-examples.R

In TKCat: Tailored Knowledge Catalog

hpof <- read_fileMDB(
   path=system.file("examples/HPO-subset", package="ReDaMoR"),
   dataModel=system.file("examples/HPO-model.json", package="ReDaMoR"),
   dbInfo=list(
      "name"="HPO",
      "title"="Data extracted from the HPO database",
      "description"=paste(
         "This is a very small subset of the HPO!",
         "Visit the reference URL for more information"
      ),
      "url"="http://human-phenotype-ontology.github.io/"
   )
)
count_records(hpof)

## The following commands take time on fileMDB object
\dontrun{

select(hpof, HPO_hp:HPO_diseases)
toTake <- "HPO_altId"
select(hpof, all_of(toTake))

hpoSlice <- slice(hpof, HPO_diseases=1:10)
count_records(hpoSlice)

if("stringr" %in% installed.packages()[,"Package"]){
   epilHP <- filter(
      hpof,
      HPO_diseases=stringr::str_detect(
         label, stringr::regex("epilepsy", ignore_case=TRUE)
      )
   )
   count_records(epilHP)
   label <- "Rolandic epilepsy"
   cn <- sym("label")
   reHP <- filter(
      hpof,
      HPO_diseases=!!cn==!!label
   )
}

}