GeneCoordsFromEntrez.R

library(biomaRt)

## How to get gene coordinates starting from Entrez gene IDs:

## Example for human:
GeneName <- "hgnc_symbol"            ## for mouse use "mgi_symbol"
DataSet  <- "hsapiens_gene_ensembl"  ## for mouse use "mmusculus_gene_ensembl

## Create a look-up table using biomaRt:
Coords <- mmusculus_genes <- getBM(attributes = c("entrezgene_id", 
                                                  "ensembl_gene_id",
                                                  GeneName,      
                                                  "chromosome_name",
                                                  "start_position",
                                                  "end_position"), 
                                   mart = useMart("ensembl", dataset = DataSet))

## merge with your genes:
example_genes <- c("6688", "2623", "1050")

## get the output table:
output.df <- merge(x = data.frame(EntrezID = example_genes),
                   y = Coords,
                   by.x = "EntrezID", by.y = "entrezgene_id")