Convert variants to GRanges.

Description

Note that the Global Alliance for Genomics and Health API uses a 0-based coordinate system. For more detail, please see GA4GH discussions such as the following:

• https://github.com/ga4gh/schemas/issues/168

• https://github.com/ga4gh/schemas/issues/121

Usage

variantsToGRanges(variants, oneBasedCoord = TRUE, slStyle = "UCSC")

Arguments

Value

GRanges

See Also

Other variants converter functions: variantsToVRanges

Examples

# Authenticated on package load from the env variable GOOGLE_API_KEY.
variants1 <- getVariants(converter=variantsToGRanges)
summary(variants1)
variants2 <- variantsToGRanges(getVariants())
print(identical(variants1, variants2))

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(GoogleGenomics)
Loading required package: GenomicAlignments
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: 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: GenomicRanges
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: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: VariantAnnotation

Attaching package: 'VariantAnnotation'

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

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GoogleGenomics/variantsToGRanges.Rd_%03d_medium.png", width=480, height=480)
> ### Name: variantsToGRanges
> ### Title: Convert variants to GRanges.
> ### Aliases: variantsToGRanges
> 
> ### ** Examples
> 
> # Authenticated on package load from the env variable GOOGLE_API_KEY.
> variants1 <- getVariants(converter=variantsToGRanges)
Error in getSearchPage("variants", body, fields, pageToken) : 
  You are not authenticated; see ?GoogleGenomics::authenticate.
Calls: getVariants -> getVariantsPage -> getSearchPage
Execution halted