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

  KEGG_dbconn()
  KEGG_dbfile()
  KEGG_dbschema(file="", show.indices=FALSE)
  KEGG_dbInfo()

Arguments

Details

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

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

KEGG_dbschema prints the schema definition of the package annotation DB.

KEGG_dbInfo prints other information about the package annotation DB.

Value

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

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

KEGG_dbschema: none (invisible NULL).

KEGG_dbInfo: none (invisible NULL).

See Also

dbGetQuery, dbConnect, dbconn, dbfile, dbschema, dbInfo

Examples

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

  KEGG_dbschema()

  KEGG_dbInfo()

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(KEGG.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


KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGG.db/KEGG_dbconn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: KEGG_dbconn
> ### Title: Collect information about the package annotation DB
> ### Aliases: KEGG_dbconn KEGG_dbfile KEGG_dbschema KEGG_dbInfo
> ### Keywords: utilities datasets
> 
> ### ** Examples
> 
>   library(DBI)
>   ## Count the number of rows in the "pathway2name" table:
>   dbGetQuery(KEGG_dbconn(), "SELECT COUNT(*) FROM pathway2name")
  COUNT(*)
1      478
> 
>   KEGG_dbschema()
CREATE TABLE metadata (
  name VARCHAR(80) PRIMARY KEY,
  value VARCHAR(255)
);
CREATE TABLE pathway2name (
  path_id CHAR(5) NOT NULL UNIQUE,              -- KEGG pathway short ID
  path_name VARCHAR(100) NOT NULL UNIQUE         -- KEGG pathway name
);
CREATE TABLE pathway2gene (
  pathway_id CHAR(8) NOT NULL,                  -- KEGG pathway long ID
  gene_or_orf_id VARCHAR(20) NOT NULL                  -- Entrez Gene or ORF ID
);
CREATE TABLE ath_NCBI_pathway2gene (
  pathway_id CHAR(8) NOT NULL,                  -- KEGG pathway long ID
  gene_or_orf_id VARCHAR(20) NOT NULL                  -- Entrez Gene or ORF ID
);
CREATE TABLE ec2go(ec_no VARCHAR(16),go_id CHAR(10));
CREATE TABLE map_counts (
  map_name VARCHAR(80) PRIMARY KEY,
  count INTEGER NOT NULL
);
CREATE TABLE map_metadata (
  map_name VARCHAR(80) NOT NULL,
  source_name VARCHAR(80) NOT NULL,
  source_url VARCHAR(255) NOT NULL,
  source_date VARCHAR(20) NOT NULL
);

> 
>   KEGG_dbInfo()
                 name                                   value
1  PATHNAMESOURCENAME                            KEGG PATHWAY
2   PATHNAMESOURCEURL    ftp://ftp.genome.jp/pub/kegg/pathway
3  PATHNAMESOURCEDATE                              2011-Mar15
4      KEGGSOURCENAME                             KEGG GENOME
5       KEGGSOURCEURL    ftp://ftp.genome.jp/pub/kegg/genomes
6      KEGGSOURCEDATE                              2011-Mar15
7     GOEXTSOURCEDATE                         2015-Sepec2go27
8     GOEXTSOURCENAME             Gene Ontology External Link
9      GOEXTSOURCEURL http://www.geneontology.org/external2go
10           DBSCHEMA                                 KEGG_DB
11            Db type                                  KEGGDb
12    DBSCHEMAVERSION                                     2.1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>