In stephenturner/annotables: Ensembl Annotation Tables

knitr::opts_chunk$set(
    cache = FALSE,
    echo = TRUE,
    message = FALSE,
    warning = FALSE)
library(annotables)

Provides tables for converting and annotating Ensembl Gene IDs.

Installation

install.packages("devtools")
devtools::install_github("stephenturner/annotables")

Rationale

Many bioinformatics tasks require converting gene identifiers from one convention to another, or annotating gene identifiers with gene symbol, description, position, etc. Sure, biomaRt does this for you, but I got tired of remembering biomaRt syntax and hammering Ensembl's servers every time I needed to do this.

This package has basic annotation information from r ensembl_version for:

Human build 38 (grch38)
Human build 37 (grch37)
Mouse (grcm38)
Rat (rnor6)
Chicken (galgal5)
Worm (wbcel235)
Fly (bdgp6)
Macaque (mmul801)

Where each table contains:

ensgene: Ensembl gene ID
entrez: Entrez gene ID
symbol: Gene symbol
chr: Chromosome
start: Start
end: End
strand: Strand
biotype: Protein coding, pseudogene, mitochondrial tRNA, etc.
description: Full gene name/description

Additionally, there are tx2gene tables that link Ensembl gene IDs to Ensembl transcript IDs.

Usage

library(annotables)

Look at the human genes table (note the description column gets cut off because the table becomes too wide to print nicely):

grch38

Look at the human genes-to-transcripts table:

grch38_tx2gene

Tables are saved in tibble format, pipe-able with dplyr:

grch38 %>% 
    dplyr::filter(biotype == "protein_coding" & chr == "1") %>% 
    dplyr::select(ensgene, symbol, chr, start, end, description) %>% 
    head %>% 
    knitr::kable(.)

Example with DESeq2 results from the airway package, made tidy with biobroom:

library(DESeq2)
library(airway)

data(airway)
airway <- DESeqDataSet(airway, design = ~cell + dex)
airway <- DESeq(airway)
res <- results(airway)

# tidy results with biobroom
library(biobroom)
res_tidy <- tidy.DESeqResults(res)
head(res_tidy)

res_tidy %>% 
    dplyr::arrange(p.adjusted) %>% 
    head(20) %>% 
    dplyr::inner_join(grch38, by = c("gene" = "ensgene")) %>% 
    dplyr::select(gene, estimate, p.adjusted, symbol, description) %>% 
    knitr::kable(.)