Get one page of search results for a particular entity type from Google Genomics.

Description

In general, use higher level methods such as getReads and getVariants instead.

Usage

getSearchPage(entityType, body, fields, pageToken)

Arguments

Value

The raw response converted from JSON to an R object.

See Also

Other page fetch functions: getReadsPage; getVariantsPage

Examples

# Authenticated on package load from the env variable GOOGLE_API_KEY.
body <- list(readGroupSetIds=list("CMvnhpKTFhDnk4_9zcKO3_YB"),
             referenceName="22",
             start=16051400, end=16051500, pageToken=NULL)
reads <- getSearchPage("reads", body, NULL, NULL)
summary(reads)

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/getSearchPage.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getSearchPage
> ### Title: Get one page of search results for a particular entity type from
> ###   Google Genomics.
> ### Aliases: getSearchPage
> 
> ### ** Examples
> 
> # Authenticated on package load from the env variable GOOGLE_API_KEY.
> body <- list(readGroupSetIds=list("CMvnhpKTFhDnk4_9zcKO3_YB"),
+              referenceName="22",
+              start=16051400, end=16051500, pageToken=NULL)
> reads <- getSearchPage("reads", body, NULL, NULL)
Error in getSearchPage("reads", body, NULL, NULL) : 
  You are not authenticated; see ?GoogleGenomics::authenticate.
Execution halted