Build annotation package org.Xx.eg.db for a non-model organism (Ovis aries)

build_org_db.R

library(AnnotationForge)
library(biomaRt)
setwd("path/to/dir")

## Get annotation data frame for Ovis aries from BiomaRt
ensembl <- useMart("ENSEMBL_MART_ENSEMBL", host="https://www.ensembl.org")

ensembl <- useDataset("oaries_gene_ensembl", mart=ensembl)
#126 oaries_gene_ensembl Sheep (texel) genes (Oar_v3.1) Oar_v3.1

attributes_gene <- c("ensembl_gene_id", "uniprot_gn_symbol", 
                    "description", "gene_biotype",
                    "chromosome_name", "start_position", 
                    "end_position")

# Load DESeq data set
load("expression_data/DESeqOBJ.RData")
ids <- rownames(counts(dds))
gene_table <- getBM(attributes = attributes_gene, values = ids, 
                    mart = ensembl)
# First column must be "GID"
names(gene_table)[1] <- "GID"
gene_table <- gene_table[!duplicated(gene_table$GID),]
head(gene_table)[,1:4]
save(gene_table, file="geneTable.RData")

## Then call the function
makeOrgPackage(gene_info=gene_table, 
               version="1.0.0",
               maintainer="Some Name <[email protected]>",
               author="<[email protected]>",
               outputDir = ".",
               tax_id="9940",
               genus="Ovis",
               species="aries")

# Install package 
# This step requires RTools
install.packages("./org.Oaries.eg.db", type="source", repos = NULL)