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REL: 1.0.0

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pan14001 committed Nov 16, 2016
0 parents commit 41c733b89696ab0c970b61ea45773a8c891650f0
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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 <pariksheet.nanda@uconn.edu>
Maintainer: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
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
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# A NAMESPACE is strictly required by R 2.14 or higher.
import(OrganismDbi)
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## .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)
}


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## 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)
```
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\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 <pariksheet.nanda@uconn.edu>. 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)
}

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