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Last data update: 2014.03.03

R: Get reads from Google Genomics.

getReads

R Documentation

Get reads from Google Genomics.

Description

This function will return all of the reads that comprise the requested genomic range, iterating over paginated results as necessary.

Usage

getReads(readGroupSetId = "CMvnhpKTFhDnk4_9zcKO3_YB", chromosome = "22",
  start = 16051400, end = 16051500, fields = NULL, converter = c)

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.
`converter`	A function that takes a list of read R objects and returns them converted to the desired type.

Details

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

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 Reads API. If a converter is passed, object(s) of the type returned by the converter will be returned by this function.

Examples

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