Annotation package for TxDb object(s)

Description

This package loads one or more TxDb objects. Such TxDb objects are an R interface to prefabricated databases contained by this package.

The names of any objects exposed by this package indicate the origin and resources exposed. So for example TxDb.Hsapiens.UCSC.hg19.knownGene would be a TxDb object, of Homo Sapiens data from UCSC build hg19 based on the knownGene Track.

Note

This data package was made from resources at BioMart on 2014-09-26 11:23:54 -0700 (Fri, 26 Sep 2014) and based on the ENSEMBL PLANTS 22 (EBI UK)

Author(s)

Marc Carlson

See Also

transcripts, transcriptsBy

Examples

## load the library
library(TxDb.Athaliana.BioMart.plantsmart22)
## list the contents that are loaded into memory
ls('package:TxDb.Athaliana.BioMart.plantsmart22')
## show the db object that is loaded by calling it's name
TxDb.Athaliana.BioMart.plantsmart22

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(TxDb.Athaliana.BioMart.plantsmart22)
Loading required package: GenomicFeatures
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: 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: GenomicRanges
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/TxDb.Athaliana.BioMart.plantsmart22/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: TxDb.Athaliana.BioMart.plantsmart22
> ### Title: Annotation package for TxDb object(s)
> ### Aliases: TxDb.Athaliana.BioMart.plantsmart22-package
> ###   TxDb.Athaliana.BioMart.plantsmart22
> ###   TxDb.Athaliana.BioMart.plantsmart22
> ### Keywords: package data
> 
> ### ** Examples
> 
> ## load the library
> library(TxDb.Athaliana.BioMart.plantsmart22)
> ## list the contents that are loaded into memory
> ls('package:TxDb.Athaliana.BioMart.plantsmart22')
[1] "TxDb.Athaliana.BioMart.plantsmart22"
> ## show the db object that is loaded by calling it's name
> TxDb.Athaliana.BioMart.plantsmart22
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Arabidopsis thaliana
# Resource URL: www.biomart.org:80
# BioMart database: plants_mart_22
# BioMart database version: ENSEMBL PLANTS 22 (EBI UK)
# BioMart dataset: athaliana_eg_gene
# BioMart dataset description: Arabidopsis thaliana genes (TAIR10 (2010-09-TAIR10))
# BioMart dataset version: TAIR10 (2010-09-TAIR10)
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 41671
# exon_nrow: 171013
# cds_nrow: 147494
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2014-09-26 11:23:54 -0700 (Fri, 26 Sep 2014)
# GenomicFeatures version at creation time: 1.17.17
# RSQLite version at creation time: 0.11.4
# DBSCHEMAVERSION: 1.0
# TaxID: 3702
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>