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Last data update: 2014.03.03

R: Get datasets in ExpressionSet format

getDatasets

R Documentation

Get datasets in ExpressionSet format

Description

Get the datasets for every platform for the given dataset identifier.

Usage

getDatasets(dataset, ...);

Arguments

dataset

Valid dataset identifier: the GEO or InSilico DB accession code.

...

Optional arguments can be passed to the function for more specific requests:

format = "CURESET"

File format in which the dataset should be returned. Possible values:

CURESET : Curated R/Bioconductor ExpressionSet.
ESET : R/Bioconductor ExpressionSet without curation.

features = "PROBE"

Type of features in which data is represented. Two possible values: "GENE" or "PROBE". By default an expression matrix containing probes is returned

norm = "ORIGINAL"

Type of normalization to use when pre-processing a dataset. Possible normalizations: "ORIGINAL", "FRMA"[1], "SCAN"[2].

curation

Specific curation used to annotate a dataset. A curation is identified by a InSilico DB Curation identifier. You can annotate datasets yourself at https://insilicodb.com/app/browse If not defined, the default curation of specified dataset will be used.

timeout = 120

Time (in seconds) to wait for the dataset, if it has to be generated.

Value

A list with a Bioconductors ExpressionSet for every platform.

References

[1] MN. McCall, BM. Bolstad, and RA. Irizarry, Frozen Robust Multi-Array Analysis (fRMA), Biostatistics, vol. 11, no. 2, pp. 242-253 , 2008.

[2] SR. Piccolo, Y. Sun, JD. Campbell, ME. Lenburg, AH. Bild, and WE. Johnson, A single-sample microarray normalization method to facilitate personalized-medicine workflows, Genomics, vol. 100, no. 6, pp. 337-344, 2012.

Examples

InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
dataset.id <- "GSE1456"
getPlatforms(dataset.id);
## [1] "GPL96" "GPL97"
esets <- getDatasets(dataset.id, norm = "ORIGINAL");
sapply(esets, annotation)
##    GPL96    	 GPL97
##    "hgu133a"   "hgu133b"

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(inSilicoDb)
Loading required package: rjson
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RCurl
Loading required package: bitops
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/inSilicoDb/getDatasets.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getDatasets
> ### Title: Get datasets in ExpressionSet format
> ### Aliases: getDatasets
> 
> ### ** Examples
> 
> InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
  INSILICODB: Welcome RPackage Tester
[1] 5296
> dataset.id <- "GSE1456"
> getPlatforms(dataset.id);
[1] "GPL96" "GPL97"
> ## [1] "GPL96" "GPL97"
> esets <- getDatasets(dataset.id, norm = "ORIGINAL");
  INSILICODB: The dataset you requested is available for download.
  INSILICODB: Dataset GSE1456, GPL96, CURESET, PROBE, ORIGINAL, 37740, RNA, Gene expression of breast cancer tissue in a large population-based cohort of Swedish patients, finished, GSE1456GPL96_RNA_ORIGINALPROBE_37740.RData