An MDB (Modeled DataBase) based on files: fileMDB

An MDB (Modeled DataBase) based on files: fileMDB

Rename tables of a fileMDB object

Usage

# S3 method for class 'chMDB'
x$i

fileMDB(
  dataFiles,
  dbInfo,
  dataModel,
  readParameters = DEFAULT_READ_PARAMS,
  collectionMembers = NULL,
  check = TRUE,
  n_max = 10,
  verbose = FALSE
)

# S3 method for class 'fileMDB'
names(x) <- value

# S3 method for class 'fileMDB'
rename(.data, ...)

# S3 method for class 'fileMDB'
x[i]

# S3 method for class 'fileMDB'
x[[i]]

# S3 method for class 'fileMDB'
x$i

# S3 method for class 'fileMDB'
as.list(x, ...)

Arguments

x

a fileMDB object

i

the index or the name of the tables to take

dataFiles

a named vector of path to data files with all(names(dataFiles) %in% names(dataModel))

dbInfo

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

dataModel

a ReDaMoR::RelDataModel object

readParameters

a list of parameters for reading the data file. (e.g. list(delim='\t', quoted_na=FALSE,))

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

n_max

maximum number of records to read for checks purpose (default: 10). See also ReDaMoR::confront_data().

verbose

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

value

new table names

.data

a fileMDB object

...

additional parameters

Value

A fileMDB object

as.list.fileMDB() returns a simple list of tibbles with all the data from the tables in x.

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.fileMDB, slice.fileMDB

Examples

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/"
  )
)
#> HPO
#> SUCCESS
#> 
#> Check configuration
#>    - Optional checks: 
#>    - Maximum number of records: 10
count_records(hpof)
#>              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 

## The following commands take time on fileMDB object
if (FALSE) {
  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
    )
  }
}