README.md

In UofABioinformaticsHub/TxDb.Drerio.Ensembl.gtf88: Annotation package for TxDb object(s)

TxDb.Drerio.Ensembl.gtf88

Package Formation

This is a TxDb package generated from v88 of the Ensembl provided gtf file. Code for package generation was

Load the required packages

library(magrittr)
library(tibble)
library(GenomicFeatures)
library(AnnotationHub)

Find the required gtf using AnnotationHub()

ah <- AnnotationHub() %>%
    subset(species == "Danio rerio") %>%
    subset(rdataclass == "GRanges") %>%
    subset(dataprovider == "Ensembl")
hubID <- "AH53505"

Obtain a GRanges object then convert this into a TxDb object

gr <- ah[[hubID]]
txdb <- makeTxDbFromGRanges(gr, taxonomyId = 7955)

Form author and metadata objects

aut <- person(c("Stephen", "M"), "Pederson", email = "[e-mail]", role = c("aut", "cre"))
md <- data.frame(value = c(`Data source` = "Ensembl", 
                            Organism = metadata(gr)$Organism,
                            `Taxonomy ID` = metadata(gr)$`Taxonomy ID`, 
                            `Resource URL` = metadata(gr)$`Data Source`, 
                            `Type of Gene ID` = "Ensembl")) %>%
   rownames_to_column("name")

Create the package

makeTxDbPackage(txdb, 
                version = "1.0.0", 
                destDir = "/home/steve/R_Packages",
                maintainer = aut, 
                author = aut, 
                pkgname = "TxDb.Drerio.Ensembl.gtf88", 
                provider = "Ensembl",
                providerVersion = "0.88")

Package Installation

This package is not currently hosted on Bioconductor, but can be installed using

source("https://bioconductor.org/biocLite.R")
biocLite(c("GenomicFeatures", "AnnotationDbi", "devtools"))
devtools::install_github("UofABioinformaticsHub/TxDb.Drerio.Ensembl.gtf88")

UofABioinformaticsHub/TxDb.Drerio.Ensembl.gtf88 documentation built on May 4, 2019, 1:07 p.m.