Query Ensembl Variant Effect Predictor

Description

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

Usage

## S4 method for signature 'character'
ensemblVEP(file, param=VEPParam(), ...)

Arguments

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.

Value

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

Author(s)

Valerie Obenchain

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() 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ensemblVEP)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: VariantAnnotation
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

variant_effect_predictor.pl not found. Ensembl VEP is not installed in your path.

Attaching package: 'ensemblVEP'

The following object is masked from 'package:Biobase':

    cache

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ensemblVEP/ensemblVEP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ensemblVEP
> ### Title: Query Ensembl Variant Effect Predictor
> ### Aliases: ensemblVEP ensemblVEP,character-method
> ### Keywords: methods
> 
> ### ** 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: 
> ##D   gr <- ensemblVEP(file)
> ##D   gr[1:3]
> ##D   
> ## 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)
Error in .getVepPath() : 
  Couldn't find variant_effect_predictor.pl in your PATH.
Calls: ensemblVEP -> ensemblVEP -> .getVepPath
Execution halted