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Last data update: 2014.03.03

R: Get one page of reads from Google Genomics.

getReadsPage

R Documentation

Get one page of reads from Google Genomics.

Description

In general, use the getReads method instead. It calls this method, returning reads from all of the pages that comprise the requested genomic range.

Usage

getReadsPage(readGroupSetId = "CMvnhpKTFhDnk4_9zcKO3_YB", chromosome = "22",
  start = 16051400, end = 16051500, fields = NULL, pageToken = NULL)

Arguments

`readGroupSetId`	The read group set 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.
`pageToken`	The page token. This can be NULL (default) for the first page.

Details

By default, this function gets reads for a small genomic region for one sample in 1,000 Genomes.

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:

Value

A two-element list is returned by the function.

reads: A list of R objects corresponding to the JSON objects returned by the Google Genomics Reads API.

nextPageToken: The token to be used to retrieve the next page of results, if applicable.

Examples

# Authenticated on package load from the env variable GOOGLE_API_KEY.
readsPage <- getReadsPage()
summary(readsPage)
summary(readsPage$reads[[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/getReadsPage.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getReadsPage
> ### Title: Get one page of reads from Google Genomics.
> ### Aliases: getReadsPage
> 
> ### ** Examples
> 
> # Authenticated on package load from the env variable GOOGLE_API_KEY.
> readsPage <- getReadsPage()
Error in getSearchPage("reads", body, fields, pageToken) : 
  You are not authenticated; see ?GoogleGenomics::authenticate.
Calls: getReadsPage -> getSearchPage
Execution halted