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Last data update: 2014.03.03

R: Get information about a dataset

getDatasetInfo

R Documentation

Get information about a dataset

Description

Get information about the availability and the default parameters of a dataset.

Usage

getDatasetInfo(dataset, platform, ...);

Arguments

dataset

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

platform

The platform of the chip on which a measurement was done. A platform is identified by its GEO 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 prefered curation of specified dataset will be used.

Details

The function getDatasetInfo has two functionalities.

Its first functionality is to return the default parameters of the given dataset if it is called with dataset and platform as only arguments.

Its second functionality is to check the availability of a dataset when optional arguments are specified. Do not forget to surround the function call by a tryCatch function when checking for availability.

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");
data.id <- "GSE781";
plt.id <- "GPL96";

## return the default parameters when calling getDataset
eset <- getDatasetInfo( data.id, plt.id);
eset$norm;
## [1] "FRMA"

plt.id <- "GPL97";

## check the availability of the normalizations
norms <- c("FRMA", "ORIGINAL")
output <- sapply(norms, function(n) {
  tryCatch({
    eset <- getDatasetInfo(data.id, plt.id, norm = n);
    eset$norm;
  }, error = function(e) {
    message(e);
  });
});
output$FRMA
## NULL
output$ORIGINAL
## [1] "ORIGINAL"

Results


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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/getDatasetInfo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getDatasetInfo
> ### Title: Get information about a dataset
> ### Aliases: getDatasetInfo
> 
> ### ** Examples
> 
> InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
  INSILICODB: Welcome RPackage Tester
[1] 5296
> data.id <- "GSE781";
> plt.id <- "GPL96";
> 
> ## return the default parameters when calling getDataset
> eset <- getDatasetInfo( data.id, plt.id);
  INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience.
Error: Stopped because of previous errors
Execution halted