Hello,

In R, I previously used this piece of code to look up Ensembl IDs for lists of genes beginning with ENSG000... .  In this example, my_df is a dataframe where the rownames are the gene IDs 9e.g. ENSG...):

  my_df$ensembl <- sapply( strsplit( rownames(my_df), split="\\+" ), "[", 1 )
  ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="www.ensembl.org") # reflects recent change to hosting, as discussed in https://support.bioconductor.org/p/74322/
  genemap <- getBM( attributes = c("ensembl_gene_id", "entrezgene", "hgnc_symbol"),
                    filters = "ensembl_gene_id",
                    values = my_df$ensembl,
                    mart = ensembl )
  idx <- match( my_df$ensembl, genemap$ensembl_gene_id )
  my_df$entrez <- genemap$entrezgene[ idx ]
  my_df$hgnc_symbol <- genemap$hgnc_symbol[ idx ]

I'd now like to use this on a dataframe where the input row names are transcript IDs (e.g. ENST000...). I'm not sure whether I can do this with BioMart - does anyone know?

you could actually use stuff from the ensembldb package to get the mapping between transcript ids and gene names (HGNC):

library(EnsDb.Hsapiens.v75)

edb <- EnsDb.Hsapiens.v75

## Get all transcripts defined in Ensembl (version 75):

tx <- transcripts(edb, columns=c("tx_id", "gene_id", "gene_name"))

## you can then extract the transcript ids and gene names or even

mapping <- cbind(tx_id=tx$tx_id, name=tx$gene_name)

rownames(mapping) <- mapping[, 1]

head(mapping)

> head(mapping)
                tx_id             name    
ENST00000373020 "ENST00000373020" "TSPAN6"
ENST00000494424 "ENST00000494424" "TSPAN6"
ENST00000496771 "ENST00000496771" "TSPAN6"
ENST00000373031 "ENST00000373031" "TNMD"  
ENST00000485971 "ENST00000485971" "TNMD"  
ENST00000371582 "ENST00000371582" "DPM1"  

hope that helps

cheers, jo