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

  mirbase_dbconn()
  mirbase_dbfile()
  mirbase_dbschema(file="", show.indices=FALSE)
  mirbase_dbInfo()

Arguments

Details

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

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

mirbase_dbschema prints the schema definition of the package annotation DB.

mirbase_dbInfo prints other information about the package annotation DB.

Value

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

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

mirbase_dbschema: none (invisible NULL).

mirbase_dbInfo: none (invisible NULL).

See Also

dbGetQuery, dbConnect, dbconn, dbfile, dbschema, dbInfo

Examples

  ## Count the number of rows in the "ID2ACC" table:
  dbGetQuery(mirbase_dbconn(), "SELECT COUNT(*) FROM mirna")

  ## The connection object returned by mirbase_dbconn() was
  ## created with:
  dbConnect(SQLite(), dbname=mirbase_dbfile(), cache_size=64000,
  synchronous=0)

  mirbase_dbschema()

  mirbase_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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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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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(mirbase.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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirbase.db/mirbase_dbconn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mirbase_dbconn
> ### Title: Collect information about the package annotation DB
> ### Aliases: mirbase_dbconn mirbase_dbfile mirbase_dbschema mirbase_dbInfo
> ### Keywords: utilities datasets
> 
> ### ** Examples
> 
>   ## Count the number of rows in the "ID2ACC" table:
>   dbGetQuery(mirbase_dbconn(), "SELECT COUNT(*) FROM mirna")
Error: could not find function "dbGetQuery"
Execution halted