diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..91dcea2 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,16 @@ +Package: TxDb.Dmelanogaster.UCSC.dm6.refGene +Title: Annotation package for TxDb object(s) +Description: Exposes an annotation databases generated from UCSC by exposing these as TxDb objects +Version: 0.01 +Author: Pariksheet Nanda [cre] +Maintainer: Pariksheet Nanda +Depends: GenomicFeatures (>= 1.26.0) +Imports: AnnotationDbi +License: Artistic-2.0 +organism: Drosophila melanogaster +species: Drosophila melanogaster +provider: UCSC +provider_version: dm6 genome based on the refGene table +release_date: 2016-11-16 13:49:13 -0500 (Wed, 16 Nov 2016) +resource_url: http://genome.ucsc.edu/ +biocViews: AnnotationData, Genetics, TxDb, Drosophila_melanogaster diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..f22bbfb --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,8 @@ +import(AnnotationDbi) +import(GenomicFeatures) + +### Don't export TxDb.Dmelanogaster.UCSC.dm6.refGene (the object defined in this +### package): it is created and dynamically exported at load time (refer +### to R/zzz.R for the details). + + diff --git a/R/zzz.R b/R/zzz.R new file mode 100644 index 0000000..9da6f4e --- /dev/null +++ b/R/zzz.R @@ -0,0 +1,17 @@ +### +### Load any db objects whenever the package is loaded. +### + +.onLoad <- function(libname, pkgname) +{ + ns <- asNamespace(pkgname) + path <- system.file("extdata", package=pkgname, lib.loc=libname) + files <- dir(path) + for(i in seq_len(length(files))){ + db <- loadDb(system.file("extdata", files[[i]], package=pkgname, + lib.loc=libname),packageName=pkgname) + objname <- sub(".sqlite$","",files[[i]]) + assign(objname, db, envir=ns) + namespaceExport(ns, objname) + } +} diff --git a/README.md b/README.md new file mode 100644 index 0000000..ac893d4 --- /dev/null +++ b/README.md @@ -0,0 +1,19 @@ +## Summary + +TxDb database for UCSC refGene table, so that you can run database +queries like: + +```R +library(TxDb.Dmelanogaster.UCSC.dm6.refGene) + +tx <- transcripts(TxDb.Dmelanogaster.UCSC.dm6.refGene, + columns = c("TXID", "TXNAME", "GENEID")) +``` + +## Installation + +```R +install.packages("devtools") +host="https://github.uconn.edu/api/v3" +devtools::install_github("CoreLab/TxDb.Dmelanogaster.UCSC.dm6.refGene", host = host) +``` diff --git a/inst/extdata/TxDb.Dmelanogaster.UCSC.dm6.refGene.sqlite b/inst/extdata/TxDb.Dmelanogaster.UCSC.dm6.refGene.sqlite new file mode 100644 index 0000000..f31d956 Binary files /dev/null and b/inst/extdata/TxDb.Dmelanogaster.UCSC.dm6.refGene.sqlite differ diff --git a/man/package.Rd b/man/package.Rd new file mode 100644 index 0000000..61e22f2 --- /dev/null +++ b/man/package.Rd @@ -0,0 +1,46 @@ +\name{TxDb.Dmelanogaster.UCSC.dm6.refGene} +\docType{package} + +\alias{TxDb.Dmelanogaster.UCSC.dm6.refGene-package} +\alias{TxDb.Dmelanogaster.UCSC.dm6.refGene} +\alias{TxDb.Dmelanogaster.UCSC.dm6.refGene} + + +\title{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 + 2016-11-16 13:49:13 -0500 (Wed, 16 Nov 2016) and based on the dm6 genome based on the refGene table +} + +\author{Pariksheet Nanda [cre]} + + +\seealso{ + \link[GenomicFeatures]{transcripts}, + \link[GenomicFeatures]{transcriptsBy} +} + +\examples{ +## load the library +library(TxDb.Dmelanogaster.UCSC.dm6.refGene) +## list the contents that are loaded into memory +ls('package:TxDb.Dmelanogaster.UCSC.dm6.refGene') +## show the db object that is loaded by calling it's name +TxDb.Dmelanogaster.UCSC.dm6.refGene + +} + +\keyword{package} +\keyword{data}