An MDB (Modeled DataBase) in memory: memoMDB

An MDB (Modeled DataBase) in memory: memoMDB

Rename tables of a memoMDB object

Usage

memoMDB(
  dataTables,
  dataModel,
  dbInfo,
  collectionMembers = NULL,
  check = TRUE,
  checks = c("unique", "not nullable", "foreign keys"),
  verbose = FALSE
)

# S3 method for memoMDB
names(x) <- value

# S3 method for memoMDB
rename(.data, ...)

# S3 method for memoMDB
[(x, i)

# S3 method for memoMDB
[[(x, i)

# S3 method for memoMDB
$(x, i)

Arguments

dataTables

a list of tibbles

dataModel

a ReDaMoR::RelDataModel object

dbInfo

a list with DB information: "name" (only mandatory field), "title", "description", "url", "version", "maintainer".

collectionMembers

the members of collections as provided to the collection_members<- function (default: NULL ==> no member).

check

logical: if TRUE (default) the data are confronted to the data model

checks

a character vector with the name of optional checks to be done (all of them c("unique", "not nullable", "foreign keys"))

verbose

if TRUE display the data confrontation report (default: FALSE)

x

a memoMDB object

value

new table names

.data

a memoMDB object

...

Use new_name = old_name to rename selected tables

i

the index or the name of the tables to take

Value

A memoMDB object

See also

• MDB methods: db_info, data_model, data_tables, collection_members, count_records, dims, filter_with_tables, as_fileMDB

• Additional general documentation is related to MDB.

• filter.memoMDB, slice.memoMDB

Examples

hpo <- 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/"
   )
) %>% 
   as_memoMDB()
#> HPO
#> SUCCESS
#> 
#> Check configuration
#>    - Optional checks: 
#>    - Maximum number of records: 10
count_records(hpo)
#>              HPO_hp           HPO_altId     HPO_sourceFiles        HPO_diseases 
#>                 500                  89                   2                1903 
#>       HPO_diseaseHP HPO_diseaseSynonyms         HPO_parents     HPO_descendants 
#>                2594                2337                  95                 972 
#>        HPO_synonyms 
#>                 730 

## Too long on win-builder.r-project.org
if (FALSE) {
   
hpoSlice <- slice(hpo, HPO_diseases=1:10)
count_records(hpoSlice)

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

}