GRanges_Reduce_Genes_2.R

library(biomaRt)

## get mouse transcript coordinates
mmusculus_genes <- getBM(attributes = c("ensembl_gene_id", "chromosome_name",
                                        "transcript_start", "transcript_end"),  
                         mart = useMart("ensembl", dataset = "mmusculus_gene_ensembl"))

## put in the exact same format as the example of the toplevel question,
## not caring about the fact that hgnc is not the correct name for mouse genes:
large.input <- data.frame(chrom = mmusculus_genes$chromosome_name,
                          start = mmusculus_genes$transcript_start,
                          end   = mmusculus_genes$transcript_end, 
                          hgnc  = mmusculus_genes$ensembl_gene_id)

## See below for benchmarks