keytypes,src_organism-method {Organism.dplyr} | R Documentation

## Using the "select" interface on src_organism objects

### Description

`select`, `columns` and `keys` can be used together to extract data from a `src_organism` object.

### Usage

    ## S4 method for signature 'src_organism'
    keytypes(x)

    ## S4 method for signature 'src_organism'
    columns(x)

    ## S4 method for signature 'src_organism'
    keys(x, keytype, ...)

    select_tbl(x, keys, columns, keytype)

    ## S4 method for signature 'src_organism'
    select(x, keys, columns, keytype)

    ## S4 method for signature 'src_organism'
    mapIds(x, keys, column, keytype, ..., multiVals)

### Arguments

`x` | a `src_organism` object
`keytype` | specifies the kind of keys that will be returned. By default keys will return the keys for schema of the `src_organism` object.
`...` | other arguments. These include: pattern: the pattern to match. column: the column to search on. fuzzy: TRUE or FALSE value. Use fuzzy matching? (this is used with pattern)
`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.
`column` | character(1) the column to search on, can only have a single element for the value
`multiVals` | What should `mapIds` do when there are multiple values that could be returned. Options include: first: when there are multiple matches only the 1st thing that comes back will be returned. This is the default behavior. list: return a list object to the end user filter: 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: return an NA value whenever there are multiple matches CharacterList: returns a SimpleCharacterList object FUN: 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)]]}`

### Details

`keytypes()`: discover which keytypes can be passed to keytype argument of methods `select` or `keys`.

`keys()`: returns keys for the `src_organism` object. By default it returns the primary keys for the database, and returns the keys from that keytype when the keytype argument is used.

`columns()`: discover which kinds of data can be returned for the `src_organism` object.

`select()`: retrieves the data as a `tibble` based on parameters for selected keys columns and keytype arguments. If requested columns that have multiple matches for the keys, 'select()' will return a `tibble` with one row for each possible match.

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

### Value

`keys`, `columns` and `keytypes` each returns a character vector of possible values. `select` returns a `tibble`.

### Author(s)

Yubo Cheng.

### See Also

`AnnotationDb-class` for more descriptsion of methods `select`, `keytypes`, `keys` and `columns`.

`src_organism` for creating a `src_organism` object.

`transcripts_tbl` for generic functions to extract genomic features from a `src_organism` object.

### Examples

    ## Not run: src <- src_organism("TxDb.Hsapiens.UCSC.hg38.knownGene")
    src <- src_organism(dbpath=hg38light())

    ## keytypes
    keytypes(src)

    ## columns
    columns(src)

    ## keys
    keys(src, "entrez")

    keytype <- "symbol"
    keys <- c("ADA", "NAT2")
    columns <- c("entrez", "tx_id", "tx_name","exon_id")

    ## select
    select_tbl(src, keys, columns, keytype)
    select(src, keys, columns, keytype)

    ## mapIds
    mapIds(src, keys, column = "tx_name", keytype)

[Package Organism.dplyr version 1.6.2 Index]