Ensembl based annotation package

Description

This package loads an SQL connection to a database containing annotations from Ensembl. For examples and help on functions see the help pages from the ensembldb package!

Note

This data package was made from resources at Ensembl on Wed Mar 18 09:30:54 2015 and based on the 75

Author(s)

J Rainer

Examples

## load the library
##library(EnsDb.Hsapiens.v75)
## list the contents that are loaded into memory
ls('package:EnsDb.Hsapiens.v75')
## show the db object that is loaded by calling it's name
EnsDb.Hsapiens.v75

## for more examples see the ensembldb package.

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(EnsDb.Hsapiens.v75)
Loading required package: ensembldb
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: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/EnsDb.Hsapiens.v75/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: EnsDb.Hsapiens.v75
> ### Title: Ensembl based annotation package
> ### Aliases: EnsDb.Hsapiens.v75-package EnsDb.Hsapiens.v75
> ###   EnsDb.Hsapiens.v75
> ### Keywords: package data
> 
> ### ** Examples
> 
> ## load the library
> ##library(EnsDb.Hsapiens.v75)
> ## list the contents that are loaded into memory
> ls('package:EnsDb.Hsapiens.v75')
[1] "EnsDb.Hsapiens.v75"
> ## show the db object that is loaded by calling it's name
> EnsDb.Hsapiens.v75
EnsDb for Ensembl:
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.1.2
|Creation time: Wed Mar 18 09:30:54 2015
|ensembl_version: 75
|ensembl_host: manny.i-med.ac.at
|Organism: homo_sapiens
|genome_build: GRCh37
|DBSCHEMAVERSION: 1.0
| No. of genes: 64102.
| No. of transcripts: 215647.
> 
> ## for more examples see the ensembldb package.
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>