Get list of all available dataset identifiers that satisfy all specified constraints (see Arguments).
Usage
getDatasetList(...);
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.
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.
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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(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/getDatasetList.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getDatasetList
> ### Title: Get list of all available dataset identifiers
> ### Aliases: getDatasetList
>
> ### ** Examples
>
> length(getDatasetList());
INSILICODB: 8033 datasets found.
[1] 8033
> ## 7167
> length(getDatasetList(platform = "GPL570"));
INSILICODB: 2788 datasets found.
[1] 2788
> ## 2717
> length(getDatasetList(platform = "GPL570", norm = "FRMA"));
INSILICODB: 2488 datasets found.
[1] 2488
> ## 2406
> length(getDatasetList(platform = "GPL570", norm = "FRMA",
+ query = "Thyroid Cancer"));
INSILICODB: 5 datasets found.
[1] 5
> ## 5
> getDatasetList(platform = "GPL570", norm = "FRMA",
+ query = "Thyroid Cancer");
INSILICODB: 5 datasets found.
[1] "GSE29265" "GSE32161" "GSE2109" "GSE7307" "GSE6004"
> ## [1] "GSE6004" "GSE7307" "GSE32161" "GSE29265" "GSE2109"
>
>
>
>
>
> dev.off()
null device
1
>