REL: 0.01

DESCRIPTION

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+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 <pariksheet.nanda@uconn.edu> [cre]
+Maintainer: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
+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

NAMESPACE

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+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).
+
+

R/zzz.R

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+###
+### 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)
+  }
+}

README.md

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+## 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)
+```

man/package.Rd

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+\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 <pariksheet.nanda@uconn.edu> [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}