convert_geneID_geneSymbols.R

# script to convert ensembl gene Id to gene symbols
# setwd("~/Desktop/demo/convert_geneID_to_gene_symbols")

library(biomaRt)
library(annotables)
library(org.Hs.eg.db)
library(EnsDb.Hsapiens.v86)
library(tidyverse)

# input list of Ensembl ID's
ensembl.ids <- read.delim('gene_ids.txt', header = F)


# method 1: biomaRt
listEnsembl()
ensembl <- useEnsembl(biomart = "genes")
datasets <- listDatasets(ensembl)

ensembl.con <- useMart("ensembl", dataset = 'hsapiens_gene_ensembl')

attr <- listAttributes(ensembl.con)
filters <- listFilters(ensembl.con)

getBM(attributes = c('ensembl_gene_id','external_gene_name'),
      filters = "ensembl_gene_id",
      values = ensembl.ids$V1,
      mart = ensembl.con)

# method 2: annotables
grch38 %>%
  filter(ensgene %in% ensembl.ids$V1)


# method 3: annotation DBs

keytypes(org.Hs.eg.db)
columns(org.Hs.eg.db)

mapIds(org.Hs.eg.db,
       keys = ensembl.ids$V1,
       keytype = 'ENSEMBL',
       column = 'SYMBOL')

keytypes(EnsDb.Hsapiens.v86)
columns(EnsDb.Hsapiens.v86)

mapIds(EnsDb.Hsapiens.v86,
       keys = ensembl.ids$V1,
       keytype = 'GENEID',
       column = 'SYMBOL')