This function will return all of the variants that comprise the requested
genomic range, iterating over paginated results as necessary.
Usage
getVariants(datasetId = "10473108253681171589", chromosome = "22",
start = 16051400, end = 16051500, fields = NULL, converter = c)
Arguments
datasetId
The dataset ID.
chromosome
The chromosome.
start
Start position on the chromosome in 0-based coordinates.
end
End position on the chromosome in 0-based coordinates.
fields
A subset of fields to retrieve. The default (NULL) will
return all fields.
converter
A function that takes a list of variant R objects and
returns them converted to the desired type.
Details
By default, this function gets variants from a small section of 1000
Genomes phase 1 variants.
Optionally pass a converter as appropriate for your use case. By passing it
to this method, only the converted objects will be accumulated in memory.
The converter function should return an empty container of the desired type
if called without any arguments.
Value
By default, the return value is a list of R objects
corresponding to the JSON objects returned by the Google Genomics
Variants API. If a converter is passed, object(s) of the type
returned by the converter will be returned by this function.
See Also
getReads for equivalent function for reads, and
variantsToVRanges for a converter function.
Examples
# Authenticated on package load from the env variable GOOGLE_API_KEY.
variants <- getVariants()
summary(variants)
summary(variants[[1]])
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/getVariants.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getVariants
> ### Title: Get variants from Google Genomics.
> ### Aliases: getVariants
>
> ### ** Examples
>
> # Authenticated on package load from the env variable GOOGLE_API_KEY.
> variants <- getVariants()
Error in getSearchPage("variants", body, fields, pageToken) :
You are not authenticated; see ?GoogleGenomics::authenticate.
Calls: getVariants -> getVariantsPage -> getSearchPage
Execution halted