AnnotationDb-objects {AnnotationDbi} | R Documentation

## AnnotationDb objects and their progeny, methods etc.

### Description

`AnnotationDb` is the virtual base class for all annotation packages. It contain a database connection and is meant to be the parent for a set of classes in the Bioconductor annotation packages. These classes will provide a means of dispatch for a widely available set of `select` methods and thus allow the easy extraction of data from the annotation packages.

`select`, `columns` and `keys` are used together to extract data from an `AnnotationDb` object (or any object derived from the parent class). Examples of classes derived from the `AnnotationDb` object include (but are not limited to): `ChipDb`, `OrgDb` `GODb`, `OrthologyDb` and `ReactomeDb`.

`columns` shows which kinds of data can be returned for the `AnnotationDb` object.

`keytypes` allows the user to discover which keytypes can be passed in to `select` or `keys` and the `keytype` argument.

`keys` returns keys for the database contained in the `AnnotationDb` object . This method is already documented in the keys manual page but is mentioned again here because it's usage with `select` is so intimate. By default it will return the primary keys for the database, but if used with the `keytype` argument, it will return the keys from that keytype.

`select` will retrieve the data as a data.frame based on parameters for selected `keys` `columns` and `keytype` arguments. Users should be warned that if you call `select` and request columns that have multiple matches for your keys, select will return a data.frame with one row for each possible match. This has the effect that if you request multiple columns and some of them have a many to one relationship to the keys, things will continue to multiply accordingly. So it's not a good idea to request a large number of columns unless you know that what you are asking for should have a one to one relationship with the initial set of keys. In general, if you need to retrieve a column (like GO) that has a many to one relationship to the original keys, it is most useful to extract that separately.

`mapIds` gets the mapped ids (column) for a set of keys that are of a particular keytype. Usually returned as a named character vector.

`saveDb` will take an AnnotationDb object and save the database to the file specified by the path passed in to the `file` argument.

`loadDb` takes a .sqlite database file as an argument and uses data in the metadata table of that file to return an AnnotationDb style object of the appropriate type.

`species` shows the genus and species label currently attached to the `AnnotationDb` objects database.

`dbfile` gets the database file associated with an object.

`dbconn` gets the datebase connection associated with an object.

`taxonomyId` gets the taxonomy ID associated with an object (if available).

### Usage

      columns(x)
      keytypes(x)
      keys(x, keytype, ...)
      select(x, keys, columns, keytype, ...)
      mapIds(x, keys, column, keytype, ..., multiVals)
      saveDb(x, file)
      loadDb(file, packageName=NA)

### Arguments

`x` | the `AnnotationDb` object. But in practice this will mean an object derived from an `AnnotationDb` object such as a `OrgDb` or `ChipDb` object.
`keys` | the keys to select records for from the database. All possible keys are returned by using the `keys` method.
`columns` | the columns or kinds of things that can be retrieved from the database. As with `keys`, all possible columns are returned by using the `columns` method.
`keytype` | the keytype that matches the keys used. For the `select` methods, this is used to indicate the kind of ID being used with the keys argument. For the `keys` method this is used to indicate which kind of keys are desired from `keys`
`column` | the column to search on (for `mapIds`). Different from `columns` in that it can only have a single element for the value
`...` | other arguments. These include: pattern: the pattern to match (used by keys) column: the column to search on. This is used by keys and is for when the thing you want to pattern match is different from the keytype, or when you want to simply want to get keys that have a value for the thing specified by the column argument. fuzzy: TRUE or FALSE value. Use fuzzy matching? (this is used with pattern by the keys method)
`multiVals` | What should `mapIds` do when there are multiple values that could be returned? Options include: first: This value means that when there are multiple matches only the 1st thing that comes back will be returned. This is the default behavior list: This will just returns a list object to the end user filter: This will remove all elements that contain multiple matches and will therefore return a shorter vector than what came in whenever some of the keys match more than one value asNA: This will return an NA value whenever there are multiple matches CharacterList: This just returns a SimpleCharacterList object FUN: You can also supply a function to the `multiVals` argument for custom behaviors. The function must take a single argument and return a single value. This function will be applied to all the elements and will serve a 'rule' that for which thing to keep when there is more than one element. So for example this example function will always grab the last element in each result: `last <- function(x){x[[length(x)]]}`
`file` | an `sqlite` file path. A string the represents the full name you want for your sqlite database and also where to put it.
`packageName` | for internal use only

### Value

`keys`,`columns` and `keytypes` each return a character vector or possible values. `select` returns a data.frame.

### Author(s)

Marc Carlson

### See Also

`keys`, `dbConnect`, `dbListTables`, `dbListFields`, `dbGetQuery`, Bimap

### Examples

    require(hgu95av2.db)
    ## display the columns
    columns(hgu95av2.db)
    ## get the 1st 6 possible keys
    keys <- head( keys(hgu95av2.db) )
    keys
    ## lookup gene symbol and gene type for the 1st 6 keys
    select(hgu95av2.db, keys=keys, columns = c("SYMBOL","GENETYPE"))

    ## get keys based on RefSeq
    keyref <- head( keys(hgu95av2.db, keytype="REFSEQ") )
    keyref
    ## list supported key types
    keytypes(hgu95av2.db)
    ## lookup gene symbol and refseq ID based on refseq IDs by setting
    ## the keytype to "REFSEQ" and passing in refseq keys:
    select(hgu95av2.db, keys=keyref, columns = c("SYMBOL","REFSEQ"),
           keytype="REFSEQ")

    keys <- head(keys(hgu95av2.db, 'ENTREZID'))
    ## get a default result (captures only the 1st element)
    mapIds(hgu95av2.db, keys=keys, column='ALIAS', keytype='ENTREZID')
    ## or use a different option
    mapIds(hgu95av2.db, keys=keys, column='ALIAS', keytype='ENTREZID',
        multiVals="CharacterList")
    ## Or define your own function
    last <- function(x){x[[length(x)]]}
    mapIds(hgu95av2.db, keys=keys, column='ALIAS', keytype='ENTREZID',
        multiVals=last)

    ## For other ways to access the DB, you can use dbfile() or dbconn() to extract
    dbconn(hgu95av2.db)
    dbfile(hgu95av2.db)

    ## Try to retrieve an associated taxonomyId
    taxonomyId(hgu95av2.db)

[Package AnnotationDbi version 1.54.1 Index]