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Select columns from AnnotationDb database

Source: R/AnnotationDb_select_class.R
AnnotationDb_select.Rd

A wrapper around [annotationDbi::select()] that can be used to import columns from the database where the keys are provided by a column in the annotation table.

Usage

AnnotationDb_select(
  database,
  key_column,
  key_type,
  database_columns,
  drop_na = TRUE,
  ...
)

Arguments

database

(character) The name of the AnnotationDbi package/object to import.

key_column

(character) The name of a column in the annotation table containing key values used to extract records from the AnnotationDbi database.

key_type

(character) The name of a column in the AnnoationDb database searched for matches to the key values.

database_columns

(character) The name of columns to import from the AnnoationDb database. Special case .all can be used to get all columns.

drop_na

(logical) Drop NA. Allowed values are limited to the following:

  • "TRUE": Remove rows where all columns of the returned database are NA.

  • "FALSE": Keep rows where all columns of the returned database are NA.

The default is TRUE.

...

Additional slots and values passed to struct_class.

Value

A AnnotationDb_select object with the following output slots:

updated(annotation_source) The updated annotations as an annotation_source object.

Details

This object makes use of functionality from the following packages:

  • dplyr

  • AnnotationDbi

Inheritance

A AnnotationDb_select object inherits the following struct classes:

[AnnotationDb_select] -> [model] -> [struct_class]

References

Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.4, https://CRAN.R-project.org/package=dplyr.

Pagès H, Carlson M, Falcon S, Li N (2023). AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor. doi:10.18129/B9.bioc.AnnotationDbi https://doi.org/10.18129/B9.bioc.AnnotationDbi, R package version 1.64.1, https://bioconductor.org/packages/AnnotationDbi.

See also

dplyr::left_join()

AnnotationDbi::select()

Examples

M <- AnnotationDb_select(
        database = "",
        key_column = "",
        key_type = "",
        database_columns = ".all",
        drop_na = FALSE)