tximport functions

convert_tx_to_gene.R

# A function (borrowed from the Sleuth documentation) for connecting Ensembl transcript names to common gene names
convert_tx_to_gene <- function(dat="drerio_gene_ensembl"){
    mart <- biomaRt::useMart(
        biomart = "ensembl",
        dataset = dat
    )
    t2g <- biomaRt::getBM(
        attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name"),
        mart = mart
    )
    t2g <- dplyr::rename(
        t2g,
        target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id, ext_gene = external_gene_name)
return(t2g)
}