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ID lookup by database

Source: R/database_lookup_class.R
database_lookup.Rd

Search a database (data.frame) for annotation matches based on values in a specified column.

Usage

database_lookup(
  query_column,
  database_column,
  database,
  include = NULL,
  suffix = NULL,
  not_found = NA,
  ...
)

Arguments

query_column

(character) The annotation table column name to use as the reference for searching the database e.g. "HMBD_ID".

database_column

(character) The database column to search for matches to the values in annoation_column.

database

(data.frame, annotation_database) A database to be searched. Can be a data.frame or a annotation_database object.

include

(character, NULL) The name of the database columns to be added to the annotations. If NULL, all columns are retained. The default is NULL.

suffix

(character, NULL) A string appended to the column names from the database. Used to distinguish columns from different databases with identical column names.If suffix = NULL then the column names are not changed. The default is NULL.

not_found

(character, numeric, logical, NULL) The returned value when there are no matches. The default is NA.

...

Additional slots and values passed to struct_class.

Value

A database_lookup object with the following output slots:

updated(annotation_source) The input annotation_source is updated with matching columns from the database.

Details

This object makes use of functionality from the following packages:

  • dplyr

Inheritance

A database_lookup object inherits the following struct classes:

database_lookup() ⭢ model() ⭢ struct_class()

References

Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.3, https://CRAN.R-project.org/package=dplyr.

Examples

M = database_lookup(
      query_column = "V1",
      database_column = "",
      database = data.frame(id=NA),
      include = NULL,
      suffix = NULL,
      not_found = NULL)