Client secrets file obtained from Google Developer Console. This
file could be for a native application or a service account. If this file
is not present, clientId and clientSecret must be provided for native
application credentials. Service account support needs version 0.1-2 or
greater of PKI.
clientId
Client ID from Google Developer Console, overridden if file
is provided.
clientSecret
Client Secret from Google Developer Console, overridden
if file is provided.
invokeBrowser
If TRUE or not provided, the default browser is invoked
with the auth URL iff the httpuv package is
installed (suggested). If FALSE, a URL is output which needs to be copy
pasted in a browser, and the resulting token needs to be pasted back into
the R session. With both the options, you will still need to login to your
Google account if not logged in already.
apiKey
Public API key that can be used to call the Genomics API for
public datasets. This method of authentication does not need you to login
to your Google account. Providing this key overrides all other arguments.
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/authenticate.Rd_%03d_medium.png", width=480, height=480)
> ### Name: authenticate
> ### Title: Configure how to authenticate for Google Genomics API.
> ### Aliases: authenticate
>
> ### ** Examples
>
> apiKey <- Sys.getenv("GOOGLE_API_KEY")
> if (!is.na(apiKey) && nchar(apiKey)>0) {
+ authenticate(apiKey=apiKey)
+ }
> ## Not run:
> ##D authenticate(file="clientSecrets.json")
> ##D authenticate(file="clientSecrets.json", invokeBrowser=FALSE)
> ##D authenticate(clientId="abc", clientSecret="xyz", invokeBrowser=FALSE)
> ## End(Not run)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.