diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..a38a52c --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,12 @@ +Package: Drosophila.melanogaster +Title: Annotation package for the Drosophila.melanogaster object +Description: Contains the Drosophila.melanogaster object to access data from several related annotation packages. +Version: 1.0.0 +Author: Pariksheet Nanda +Maintainer: Pariksheet Nanda +Depends: R (>= 1.6), AnnotationDbi (>= 1.17.11), methods, OrganismDbi, GenomicFeatures, GO.db, org.Dm.eg.db, TxDb.Dmelanogaster.UCSC.dm6.refGene +Imports: GenomicFeatures, AnnotationDbi +License: Artistic-2.0 +organism: Drosophila melanogaster +species: Drosophila melanogaster +biocViews: AnnotationData, Genetics, OrganismDb, Drosophila_melanogaster diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..cd1c973 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,2 @@ +# A NAMESPACE is strictly required by R 2.14 or higher. +import(OrganismDbi) diff --git a/R/zzz.R b/R/zzz.R new file mode 100644 index 0000000..488a75d --- /dev/null +++ b/R/zzz.R @@ -0,0 +1,9 @@ +## .onLoad gets the data.frame from the /data directory +.onLoad <- function(libname, pkgname) { + load(system.file("data","graphInfo.rda",package=pkgname, + lib.loc=libname)) + OrganismDbi:::.loadOrganismDbiPkg(pkgname=pkgname, + graphInfo=graphInfo) +} + + diff --git a/README.md b/README.md new file mode 100644 index 0000000..71d995f --- /dev/null +++ b/README.md @@ -0,0 +1,20 @@ +## Summary + +Combines GO, TxDb and OrgDb databases, so that you can run database +queries like: + +```R +library(Drosophila.melanogaster) + +tx <- transcripts(Drosophila.melanogaster, + columns = c("TXID", "TXNAME", "GENEID", "ENSEMBL")) +``` + +## Installation + +```R +install.packages("devtools") +host="https://github.uconn.edu/api/v3" +devtools::install_github("CoreLab/TxDb.Dmelanogaster.UCSC.dm6.refGene", host = host) +devtools::install_github("CoreLab/Drosophila.melanogaster", host = host) +``` diff --git a/data/graphInfo.rda b/data/graphInfo.rda new file mode 100644 index 0000000..d25d39e Binary files /dev/null and b/data/graphInfo.rda differ 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/Drosophila.melanogaster.Rd b/man/Drosophila.melanogaster.Rd new file mode 100644 index 0000000..82e9c23 --- /dev/null +++ b/man/Drosophila.melanogaster.Rd @@ -0,0 +1,26 @@ +\name{Drosophila.melanogaster} +\docType{data} +\alias{Drosophila.melanogaster} +\title{Annotation package that collates several annotation resources.} +\description{This data object was automatically created by Pariksheet Nanda . It + represents a collection of annotation packages that can be used as a + single object named Drosophila.melanogaster. This object can be used with the + standard four accessor method for all AnnotationDbi objects. Namely: + \code{cols}, \code{keytype}, \code{keys} and \code{select}. Users are + encouraged to read the vignette from the \code{OrganismDbi} package for + more details.} +\usage{library(Drosophila.melanogaster)} +\keyword{datasets} +\examples{ + Drosophila.melanogaster + cls <- columns(Drosophila.melanogaster) + cls + cls <- cls[c(1,19,45)] + kts <- keytypes(Drosophila.melanogaster) + kt <- kts[2] + kts + ks <- head(keys(Drosophila.melanogaster, keytype=kts[2])) + ks + res <- select(Drosophila.melanogaster, keys=ks, columns=cls, keytype=kt) + head(res) +}