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

  reactome_dbconn()
  reactome_dbfile()
  reactome_dbschema(file="", show.indices=FALSE)
  reactome_dbInfo()

Arguments

Details

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

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

reactome_dbschema prints the schema definition of the package annotation DB.

reactome_dbInfo prints other information about the package annotation DB.

Value

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

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

reactome_dbschema: none (invisible NULL).

reactome_dbInfo: none (invisible NULL).

See Also

dbGetQuery, dbConnect, dbconn, dbfile, dbschema, dbInfo

Examples

  library(RSQLite)
  ## Count the number of rows in the "pathway2name" table:
  dbGetQuery(reactome_dbconn(), "SELECT COUNT(*) FROM pathway2name")

  ## The connection object returned by reactome_dbconn() was
  ## created with:
  dbConnect(SQLite(), dbname=reactome_dbfile(), cache_size=64000,
  synchronous="off")

  reactome_dbschema()

  reactome_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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
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(reactome.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/reactome.db/reactome_dbconn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: reactome_dbconn
> ### Title: Collect information about the package annotation DB
> ### Aliases: reactome_dbconn reactome_dbfile reactome_dbschema
> ###   reactome_dbInfo
> ### Keywords: utilities datasets
> 
> ### ** Examples
> 
>   library(RSQLite)
Loading required package: DBI
>   ## Count the number of rows in the "pathway2name" table:
>   dbGetQuery(reactome_dbconn(), "SELECT COUNT(*) FROM pathway2name")
  COUNT(*)
1    41600
> 
>   ## The connection object returned by reactome_dbconn() was
>   ## created with:
>   dbConnect(SQLite(), dbname=reactome_dbfile(), cache_size=64000,
+   synchronous="off")
<SQLiteConnection>
> 
>   reactome_dbschema()

Warning messages:
1: In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
2: In max(ii) : no non-missing arguments to max; returning -Inf
> 
>   reactome_dbInfo()
                name                                        value
1           DBSCHEMA                                  REACTOME_DB
2    DBSCHEMAVERSION                                           56
3         SOURCENAME                                     Reactome
4          SOURCEURL http://www.reactome.org/pages/download-data/
5         SOURCEDATE                                   2016-04-07
6 Supporting package                                AnnotationDbi
7            Db type                                   ReactomeDb
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>