Annotation package for FeatureDb object(s)

Description

This package loads one or more FeatureDb objects. Such FeatureDb 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 TranscriptDb object, of Homo Sapiens data from UCSC build hg19 based on the knownGene Track.

Note

This data package was made from resources at UCSC on 2012-09-10 13:15:01 -0700 (Mon, 10 Sep 2012) and based on the hg19 genome based on the tRNAs table

Author(s)

Marc Carlson

See Also

transcripts, transcriptsBy

Examples

## load the library
library(FDb.UCSC.tRNAs)
## list the contents that are loaded into memory
ls('package:FDb.UCSC.tRNAs')
## show the db object that is loaded by calling it's name
FDb.Hsapiens.UCSC.hg19.tRNAs

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(FDb.UCSC.tRNAs)
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/FDb.UCSC.tRNAs/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FDb.UCSC.tRNAs
> ### Title: Annotation package for FeatureDb object(s)
> ### Aliases: FDb.UCSC.tRNAs-package FDb.UCSC.tRNAs FDb.UCSC.tRNAs
> ###   FDb.Hsapiens.UCSC.hg19.tRNAs FDb.Hsapiens.UCSC.hg18.tRNAs
> ###   FDb.Mmusculus.UCSC.mm9.tRNAs FDb.Rnorvegicus.UCSC.rn4.tRNAs
> ### Keywords: package data
> 
> ### ** Examples
> 
> ## load the library
> library(FDb.UCSC.tRNAs)
> ## list the contents that are loaded into memory
> ls('package:FDb.UCSC.tRNAs')
[1] "FDb.Hsapiens.UCSC.hg18.tRNAs"   "FDb.Hsapiens.UCSC.hg19.tRNAs"  
[3] "FDb.Mmusculus.UCSC.mm9.tRNAs"   "FDb.Rnorvegicus.UCSC.rn4.tRNAs"
> ## show the db object that is loaded by calling it's name
> FDb.Hsapiens.UCSC.hg19.tRNAs
FeatureDb object:
| Db type: FeatureDb
| Supporting package: GenomicFeatures
| data_nrow: 625
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2012-09-10 13:15:01 -0700 (Mon, 10 Sep 2012)
| GenomicFeatures version at creation time: 1.9.39
| RSQLite version at creation time: 0.11.1
| DBSCHEMAVERSION: 1.0
| Data source: UCSC
| Genome: hg19
| UCSC Table: tRNAs
| Genus and Species: Homo sapiens
| Resource URL: http://genome.ucsc.edu/

Please see: help('select') for usage information
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> dev.off()
null device 
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