VEPFlags-class: VEPFlag objects

In ensemblVEP: R Interface to Ensembl Variant Effect Predictor

Description

VEPFlags stores runtime options for the Ensembl Variant Effect Predictor.

Details

• The VEPFlags family of objects stores runtime options for querying the Ensembl Variant Effect Predictor (VEP). For complete details, see the Ensembl VEP web page.

  http://uswest.ensembl.org/info/docs/tools/vep/script/vep_options.html

Runtime options

For a description of runtime options for the most current version of the API see the ?runtimeOptions man page or the Ensembl web site:

http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html

Runtime options for archived versions can be found on the corresponding archive page.

Constructor

VEPFlags(version=max(unlist(currentVEP())), scriptPath=character(), flags=list(), ...) Creates a VEPFlags object.

version

Numeric specifying the Ensembl API version(s) supported.

flags

list of runtime options

scriptPath

character path to variant_effect_predictor.pl script; applicable when multiple versions of the script are installed locally

Accessors

In the following code, x is a VEPFlags object and value is a named list or character vector.

flags(x), flags(x) <- value

Helper functions

currentVEP(): Invoked with no arguments. Returns the most current VEPFlags class and supported Ensembl API versions.

supportedVEP(): Invoked with no arguments. Returns a list of VEPParam and VEPFlags subclasses and the Ensembl API versions they support.

The following functions create a list of runtime options and are used in the VEPFlags constructor.

flagOpts(version, ...)

Author(s)

Lori Shepherd

See Also

• The runtimeOptions man page.

• The ensemblVEP function man page.

• The VEPParam class page for archieved API verisons.

Examples

  ## -----------------------------------------------------------------------
  ## Current API version
  ## -----------------------------------------------------------------------
  ## The default constructor supports the most current version
  ## of the Ensembl variant API.
  param <- VEPFlags()
  class(param)

  ## The 'version' slot lists all API versions supported by the class.
  version(param)

  ## The 'supportedVEP' helper returns a list of VEPParam and VEPFlags
  ## classes and the corresponding API versions it support.
  supportedVEP()

  ## -----------------------------------------------------------------------
  ## Archived API versions
  ## -----------------------------------------------------------------------
  ## Create a VEPParam for an archived version by supplying the
  ## version to the constructor.
  ## See ?VEPParam for more details

  ## Note on host: A host is not assigned by default and therefore will
  ## use the VEP host default of "ensembldb.ensembl.org". Users in the
  ## US may find connection and transfer speeds quicker using our East
  ## coast mirror, "useastdb.ensembl.org"
  param <- VEPFlags(flags=list(host="useastdb.ensembl.org"))

  ## By default the VEP script used is the one found in the PATH.
  ## To specify a script in a non-standard location use the 'scriptPath'
  ## setter. Include the full path and the name of the script with the
  ## .pl extension.
  ## Not run: 
  scriptPath(param) <- "fullPathToScript/vep.pl"
  
## End(Not run)

  ## -----------------------------------------------------------------------
  ## Manipulation
  ## -----------------------------------------------------------------------

  ## View the runtime values in 'flags'.
  flags(param)

  ## Change the value of the 'everything' to TRUE.
  flags(param)$everything
  flags(param)$everything <- TRUE
  flags(param)$everything

  ## Replace multiple values using a named list.
  flags(param) <- list(verbose=TRUE, config="myconfig.txt")
  flags(param)

  ## Write the output to myfile.vcf instead of returning a VCF object.
  ## Return the sift and polyphen predictions only (not scores).
  param <- VEPFlags(flags=list(output_file="path/myfile.vcf",
		    sift="p", polyphen="p"))

  ## 'sift' and 'polyphen' are runtime options that require
  ## a character value, (i.e., 's', 'p', or 'b').
  flags(param)$sift

ensemblVEP documentation built on March 16, 2021, 6:01 p.m.