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 UCSC on 2015-03-19 13:57:20 -0700 (Thu, 19 Mar 2015) and based on the hg38 genome based on the knownGene table

Author(s)

Marc Carlson

See Also

transcripts, transcriptsBy

Examples

## load the library
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
## list the contents that are loaded into memory
ls('package:TxDb.Hsapiens.UCSC.hg38.knownGene')
## show the db object that is loaded by calling it's name
TxDb.Hsapiens.UCSC.hg38.knownGene

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)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
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.Hsapiens.UCSC.hg38.knownGene/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: TxDb.Hsapiens.UCSC.hg38.knownGene
> ### Title: Annotation package for TxDb object(s)
> ### Aliases: TxDb.Hsapiens.UCSC.hg38.knownGene-package
> ###   TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene
> ### Keywords: package data
> 
> ### ** Examples
> 
> ## load the library
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
> ## list the contents that are loaded into memory
> ls('package:TxDb.Hsapiens.UCSC.hg38.knownGene')
[1] "TxDb.Hsapiens.UCSC.hg38.knownGene"
> ## show the db object that is loaded by calling it's name
> TxDb.Hsapiens.UCSC.hg38.knownGene
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: hg38
# Organism: Homo sapiens
# UCSC Table: knownGene
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Entrez Gene ID
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 104178
# exon_nrow: 327656
# cds_nrow: 250176
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-03-19 13:57:20 -0700 (Thu, 19 Mar 2015)
# GenomicFeatures version at creation time: 1.19.32
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
# TaxID: 9606
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>