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Last data update: 2014.03.03

R: Get annotation information

getAnnotations

R Documentation

Get annotation information

Description

Get annotation information for a given dataset identifier in Bioconductors AnnotatedDataFrame format.

Usage

getAnnotations(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:

platform: The platform of the chip on which a measurement was done. A platform is identified by its GEO accession code.
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.

Value

A Bioconductors AnnotatedDataFrame.

Examples


annot <- getAnnotations("GSE4635");
pData(annot);
##             Anatomical Site  Smoker
## GSM15729    bronchus         never
## GSM104072   bronchus         current
## ...

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.
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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/getAnnotations.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getAnnotations
> ### Title: Get annotation information
> ### Aliases: getAnnotations
> 
> ### ** Examples
> 
> 
> annot <- getAnnotations("GSE4635");
> pData(annot);
                  Smoker               tissue status  age race    sex pkyrs
GSM15729    never smoker Bronchial Epithelium   NILL NILL NILL   NILL  NILL
GSM104072 current smoker Bronchial Epithelium   NILL NILL NILL   NILL  NILL
GSM104074 current smoker Bronchial Epithelium   NILL NILL NILL   NILL  NILL
GSM104075 current smoker Bronchial Epithelium    SNC   45  AFA Female    14
GSM104076 current smoker Bronchial Epithelium   NILL NILL NILL   NILL  NILL
GSM104078   never smoker Bronchial Epithelium   NILL NILL NILL   NILL  NILL
GSM104080   never smoker Bronchial Epithelium   NILL NILL NILL   NILL  NILL
GSM104082   never smoker Bronchial Epithelium   NILL NILL NILL   NILL  NILL
                                history patient_id New Columnasdfadsf
GSM15729                           NILL       NILL               NULL
GSM104072                          NILL       NILL               NULL
GSM104074                          NILL       NILL               NULL
GSM104075 current smoker without cancer        406               NULL
GSM104076                          NILL       NILL               NULL
GSM104078                          NILL       NILL               NULL
GSM104080                          NILL       NILL               NULL
GSM104082                          NILL       NILL               NULL
> ##             Anatomical Site  Smoker
> ## GSM15729    bronchus         never
> ## GSM104072   bronchus         current
> ## ...
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>