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

  illuminaRatv1_dbconn()
  illuminaRatv1_dbfile()
  illuminaRatv1_dbschema(file="", show.indices=FALSE)
  illuminaRatv1_dbInfo()

Arguments

Details

illuminaRatv1_dbconn returns a connection object to the package annotation DB. IMPORTANT: Don't call dbDisconnect on the connection object returned by illuminaRatv1_dbconn or you will break all the AnnDbObj objects defined in this package!

illuminaRatv1_dbfile returns the path (character string) to the package annotation DB (this is an SQLite file).

illuminaRatv1_dbschema prints the schema definition of the package annotation DB.

illuminaRatv1_dbInfo prints other information about the package annotation DB.

Value

illuminaRatv1_dbconn: a DBIConnection object representing an open connection to the package annotation DB.

illuminaRatv1_dbfile: a character string with the path to the package annotation DB.

illuminaRatv1_dbschema: none (invisible NULL).

illuminaRatv1_dbInfo: none (invisible NULL).

See Also

dbGetQuery, dbConnect, dbconn, dbfile, dbschema, dbInfo

Examples

  ## Count the number of rows in the "probes" table:
  dbGetQuery(illuminaRatv1_dbconn(), "SELECT COUNT(*) FROM probes")

  illuminaRatv1_dbschema()

  illuminaRatv1_dbInfo()

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)

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> library(illuminaRatv1.db)
Loading required package: AnnotationDbi
Loading required package: stats4
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

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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

Loading required package: org.Rn.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaRatv1.db/illuminaRatv1_dbconn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaRatv1_dbconn
> ### Title: Collect information about the package annotation DB
> ### Aliases: illuminaRatv1_dbconn illuminaRatv1_dbfile
> ###   illuminaRatv1_dbschema illuminaRatv1_dbInfo
> ### Keywords: utilities datasets
> 
> ### ** Examples
> 
>   ## Count the number of rows in the "probes" table:
>   dbGetQuery(illuminaRatv1_dbconn(), "SELECT COUNT(*) FROM probes")
Error: could not find function "dbGetQuery"
Execution halted