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Last data update: 2014.03.03

R: Get a list of (dataset, platform) tuples

getDatasetPlatformList

R Documentation

Get a list of (dataset, platform) tuples

Description

Get list of all available dataset and platform tuples that satisfy all specified constraints (see Arguments).

Usage

getDatasetPlatformList(...);

Arguments

...

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

platform: The platform of the chip on which a measurement was done. A platform is identified by its GEO accession code. If specified, only datasets on the given platform are returned.
norm: Type of normalization to use when pre-processing a dataset. Possible values: "ORIGINAL", "FRMA"[1], "SCAN"[2]. If specified, only datasets for which the given preprocessed data is available are returned.
query: If specified, only datasets for which the query keyword appears in either the title or description of the dataset. typical example queries are 'Thyroid Cancer', 'Primary vs Metastasis', 'p53', etc.
curated: If curated = TRUE is specified, only manually curated datasets will be returned.

Value

A list of dataset and platform tuples.

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

length(getDatasetPlatformList());
## 7167
length(getDatasetPlatformList(platform = "GPL570"));
## 2717
length(getDatasetPlatformList(platform = "GPL570", norm = "FRMA"));
## 2406
length(getDatasetPlatformList(platform = "GPL570", norm = "FRMA", 
                              query = "Thyroid Cancer"));
## 5
getDatasetPlatformList(platform = "GPL570", norm = "FRMA",
                       query = "Thyroid Cancer");
## [[1]]
## [1] "GSE6004" "GPL570" 
## 
## [[2]]
## [1] "GSE7307" "GPL570" 
## 
## [[3]]
## [1] "GSE32161" "GPL570"  
## 
## [[4]]
## [1] "GSE29265" "GPL570"  
## 
## [[5]]
## [1] "GSE2109" "GPL570"

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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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/getDatasetPlatformList.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getDatasetPlatformList
> ### Title: Get a list of (dataset, platform) tuples
> ### Aliases: getDatasetPlatformList
> 
> ### ** Examples
> 
> length(getDatasetPlatformList());
  INSILICODB: 8033 datasets found.
[1] 8033
> ## 7167
> length(getDatasetPlatformList(platform = "GPL570"));
  INSILICODB: 2788 datasets found.
[1] 2788
> ## 2717
> length(getDatasetPlatformList(platform = "GPL570", norm = "FRMA"));
  INSILICODB: 2488 datasets found.
[1] 2488
> ## 2406
> length(getDatasetPlatformList(platform = "GPL570", norm = "FRMA", 
+                               query = "Thyroid Cancer"));
  INSILICODB: 5 datasets found.
[1] 5
> ## 5
> getDatasetPlatformList(platform = "GPL570", norm = "FRMA",
+                        query = "Thyroid Cancer");
  INSILICODB: 5 datasets found.
[[1]]
[1] "GSE29265" "GPL570"  

[[2]]
[1] "GSE32161" "GPL570"  

[[3]]
[1] "GSE2109" "GPL570" 

[[4]]
[1] "GSE7307" "GPL570" 

[[5]]
[1] "GSE6004" "GPL570" 

> ## [[1]]
> ## [1] "GSE6004" "GPL570" 
> ## 
> ## [[2]]
> ## [1] "GSE7307" "GPL570" 
> ## 
> ## [[3]]
> ## [1] "GSE32161" "GPL570"  
> ## 
> ## [[4]]
> ## [1] "GSE29265" "GPL570"  
> ## 
> ## [[5]]
> ## [1] "GSE2109" "GPL570" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>