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
2015-10-07 18:10:09 +0000 (Wed, 07 Oct 2015) and based on the hg18 genome based on the knownGene table
Author(s)
Marc Carlson, Bioconductor Package Maintainer <maintainer@bioconductor.org> [cre]
See Also
transcripts,
transcriptsBy
Examples
## load the library
library(TxDb.Hsapiens.UCSC.hg18.knownGene)
## list the contents that are loaded into memory
ls('package:TxDb.Hsapiens.UCSC.hg18.knownGene')
## show the db object that is loaded by calling it's name
TxDb.Hsapiens.UCSC.hg18.knownGene
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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'help.start()' for an HTML browser interface to help.
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> library(TxDb.Hsapiens.UCSC.hg18.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.hg18.knownGene/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: TxDb.Hsapiens.UCSC.hg18.knownGene
> ### Title: Annotation package for TxDb object(s)
> ### Aliases: TxDb.Hsapiens.UCSC.hg18.knownGene-package
> ### TxDb.Hsapiens.UCSC.hg18.knownGene TxDb.Hsapiens.UCSC.hg18.knownGene
> ### Keywords: package data
>
> ### ** Examples
>
> ## load the library
> library(TxDb.Hsapiens.UCSC.hg18.knownGene)
> ## list the contents that are loaded into memory
> ls('package:TxDb.Hsapiens.UCSC.hg18.knownGene')
[1] "TxDb.Hsapiens.UCSC.hg18.knownGene"
> ## show the db object that is loaded by calling it's name
> TxDb.Hsapiens.UCSC.hg18.knownGene
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: hg18
# Organism: Homo sapiens
# Taxonomy ID: 9606
# 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: 66803
# exon_nrow: 266688
# cds_nrow: 221991
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-07 18:10:09 +0000 (Wed, 07 Oct 2015)
# GenomicFeatures version at creation time: 1.21.30
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
>
>
>
>
>
>
> dev.off()
null device
1
>