ensemblVEP (version 1.12.0)

ensemblVEP: Query Ensembl Variant Effect Predictor

Description

Retrieve variant annotation data from the Ensembl Variant Effect Predictor (VEP).

Usage

"ensemblVEP"(file, param=VEPParam(), ...)

Arguments

file

A character specifying the full path to the file, including the file name.

Valid input file types are described on the Ensembl VEP web page. http://www.ensembl.org/info/docs/variation/vep/vep_script.html#running

param

An instance of VEPParam specifying runtime options.

...

Additional arguments passed to methods.

Value

Default behavior returns a GRanges object. Options can be set to return a VCF object or write a file to disk.

Details

The Ensembl VEP tool is described in detail on the home page (link in `see also` section). The ensemblVEP function wraps the perl API and requires a local install of the Ensembl VEP available in the user's path. The VEPParam class provides a way to specify runtime options. Results are returned from Ensembl VEP as GRanges (default) or VCF objects. Alternatively, results can be written directly to a file.

References

Ensembl VEP Home: http://www.ensembl.org/info/docs/tools/vep/index.html

Human Genome Variation Society (hgvs): http://www.hgvs.org/mutnomen/

See Also

VEPParam-class

Examples

  ## -----------------------------------------------------------------------
  ## Results returned as GRanges or VCF objects
  ## -----------------------------------------------------------------------
  ## The default behavior returns a GRanges with the consequence
  ## data as metadata columns.
  file <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") 
  ## Not run: 
#   gr <- ensemblVEP(file)
#   gr[1:3]
#   ## End(Not run)
  ## When the 'vcf' option is TRUE, a VCF object is returned.
  myparam <- VEPParam(dataformat=c(vcf=TRUE))
  vcf <- ensemblVEP(file, param=myparam)
  vcf
 
  ## The consequence data are returned as the 'CSQ' column in info.
  info(vcf)$CSQ
 
  ## To parse this column use parseCSQToGRanges().
  csq <- parseCSQToGRanges(vcf)
  head(csq, 4)
 
  ## The columns returned are controlled by the 'fields' option. 
  ## By default all fields are returned. See ?VEPParam for details.
 
  ## When comparing ensemblVEP() results to the data in the
  ## input vcf we see variant 20:1230237 was not returned.
  vcf_input <- readVcf(file, "hg19")
  rowRanges(vcf_input)
  rowRanges(vcf)
 
  ## This variant has no alternate allele and is called a
  ## monomorphic reference. The Ensembl VEP automatically
  ## drops these variants. 
  rowRanges(vcf)[,c("REF", "ALT")]
 
  ## -----------------------------------------------------------------------
  ## Results written to disk
  ## -----------------------------------------------------------------------
  ## Write a file to disk by providing a path and file name as 'output_file'.
  ## Different output file formats are specified using the 'dataformat' 
  ## runtime options.
 
  ## Write a vcf file to myfile.vcf:
  myparam <- VEPParam(dataformat=c(vcf=TRUE), 
                      input=c(output_file="/path/myfile.vcf"))
  ## Write a gvf file to myfile.gvf:
  myparam <- VEPParam(dataformat=c(gvf=TRUE), 
                      input=c(output_file="/path/myfile.gvf"))
 
  ## -----------------------------------------------------------------------
  ## Runtime options
  ## -----------------------------------------------------------------------
  ## All runtime options are controlled by specifying a VEPParam.
  ## See ?VEPParam for complete details.
  param <- VEPParam()
 
  ## Logical options are turned on/off with TRUE/FALSE. By
  ## default, 'quiet' is FALSE.
  basic(param)$quiet
 
  ## Setting 'quiet' to TRUE will suppress all status and warnings.
  basic(param)$quiet <- TRUE
 
  ## Characater options are turned on/off by specifying a character 
  ## value or an empty character (i.e., character()). By default no 
  ## 'sift' results are returned.
  output(param)$sift
 
  ## Setting 'sift' to 'b' will return both predictions and scores.
  output(param)$sift <- 'b'
 
  ## Return 'sift' to the original state of no results returned.
  output(param)$sift <- character()