Collect information about the package annotation DB

Description

Some convenience functions for getting a connection object to (or collecting information about) the package annotation DB.

Usage

  lumiRatIDMapping_dbconn()
  lumiRatIDMapping_dbfile()
  lumiRatIDMapping_dbInfo()

Details

lumiRatIDMapping_dbconn returns a connection object to the package annotation DB. IMPORTANT: Don't call dbDisconnect on the connection object returned by lumiRatIDMapping_dbconn or you will break all the AnnDbObj objects defined in this package!

lumiRatIDMapping_dbfile returns the path (character string) to the package annotation DB (this is an SQLite file).

lumiRatIDMapping_dbInfo prints other information about the package annotation DB.

Value

lumiRatIDMapping_dbconn: a DBIConnection object representing an open connection to the package annotation DB.

lumiRatIDMapping_dbfile: a character string with the path to the package annotation DB.

lumiRatIDMapping_dbInfo: none (invisible NULL).

See Also

dbConnect

Examples

  ## Show the database information (meta data)
  lumiRatIDMapping_dbInfo()  

  ## List the tables included in the database
  conn <- lumiRatIDMapping_dbconn()
  dbListTables(conn)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(lumiRatIDMapping)
Loading required package: lumi
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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumiRatIDMapping/lumiRatIDMapping_dbconn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiRatIDMapping_dbconn
> ### Title: Collect information about the package annotation DB
> ### Aliases: lumiRatIDMapping_dbconn lumiRatIDMapping_dbfile
> ###   lumiRatIDMapping_dbInfo
> ### Keywords: utilities datasets
> 
> ### ** Examples
> 
>   ## Show the database information (meta data)
>   lumiRatIDMapping_dbInfo()  
            name             value
1 REFSEQ VERSION                  
2       ORGANISM Rattus norvegicus
3        SPECIES               Rat
4   MANUFACTURER          Illumina
> 
>   ## List the tables included in the database
>   conn <- lumiRatIDMapping_dbconn()
>   dbListTables(conn)
Error: could not find function "dbListTables"
Execution halted