seqlevelsStyle {ensembldb} | R Documentation

## Support for other than Ensembl seqlevel style

### Description

The methods and functions on this help page allow to integrate `EnsDb` objects and the annotations they provide with other Bioconductor annotation packages that base on chromosome names (seqlevels) that are different from those defined by Ensembl.

### Usage

    ## S4 method for signature 'EnsDb'
    seqlevelsStyle(x)

    ## S4 replacement method for signature 'EnsDb'
    seqlevelsStyle(x) <- value

    ## S4 method for signature 'EnsDb'
    supportedSeqlevelsStyles(x)

### Arguments

(In alphabetic order)

`value` | For `seqlevelsStyle<-`: a character string specifying the seqlevels style that should be set. Use the `supportedSeqlevelsStyle` to list all available and supported seqlevel styles.
`x` | An `EnsDb` instance.

### Value

For `seqlevelsStyle`: see method description above.

For `supportedSeqlevelsStyles`: see method description above.

### Methods and Functions

seqlevelsStyle

  Get the style of the seqlevels in which results returned from the `EnsDb` object are encoded. By default, and internally, seqnames as provided by Ensembl are used.

  The method returns a character string specifying the currently used seqlevelstyle.

seqlevelsStyle<-

  Change the style of the seqlevels in which results returned from the `EnsDb` object are encoded. Changing the seqlevels helps integrating annotations from `EnsDb` objects e.g. with annotations from packages that base on UCSC annotations.

supportedSeqlevelsStyles

  Lists all seqlevel styles for which mappings between seqlevel styles are available in the `GenomeInfoDb` package.

  The method returns a character vector with supported seqlevel styles for the organism of the `EnsDb` object.

### Note

The mapping between different seqname styles is performed based on data provided by the `GenomeInfoDb` package. Note that in most instances no mapping is provided for seqnames other than for primary chromosomes. By default functions from the `ensembldb` package return the original seqname is in such cases. This behaviour can be changed with the `ensembldb.seqnameNotFound` global option. For the special keyword `"ORIGINAL"` (the default), the original seqnames are returned, for `"MISSING"` an error is thrown if a seqname can not be mapped. In all other cases, the value of the option is returned as seqname if no mapping is available (e.g. setting `options(ensembldb.seqnameNotFound=NA)` returns an `NA` if the seqname is not mappable).

### Author(s)

Johannes Rainer

### See Also

`EnsDb` `transcripts`

### Examples

    library(EnsDb.Hsapiens.v86)
    edb <- EnsDb.Hsapiens.v86

    ## Get the internal, default seqlevel style.
    seqlevelsStyle(edb)

    ## Get the seqlevels from the database.
    seqlevels(edb)

    ## Get all supported mappings for the organism of the EnsDb.
    supportedSeqlevelsStyles(edb)

    ## Change the seqlevels to UCSC style.
    seqlevelsStyle(edb) <- "UCSC"
    seqlevels(edb)

    ## Change the option ensembldb.seqnameNotFound to return NA in case
    ## the seqname can not be mapped form Ensembl to UCSC.
    options(ensembldb.seqnameNotFound = NA)

    seqlevels(edb)

    ## Restoring the original setting.
    options(ensembldb.seqnameNotFound = "ORIGINAL")

[Package ensembldb version 2.10.2 Index]