transcript2gene {BUSpaRse} | R Documentation

## Map Ensembl transcript ID to gene ID

### Description

This function is a shortcut to get the correctly sorted data frame with transcript IDs and the corresponding gene IDs from Ensembl biomart or Ensembl transcriptome FASTA files. For biomart query, it calls `tr2g_ensembl` and then `sort_tr2g`. For FASTA files, it calls `tr2g_fasta` and then `sort_tr2g`. Unlike in `tr2g_ensembl` and `tr2g_fasta`, multiple species can be supplied if cells from different species were sequenced together. This function should only be used if the kallisto inidex was built with transcriptomes from Ensembl. Also, if querying biomart, please make sure to set `ensembl_version` to match the version where the transcriptomes were downloaded.

### Usage

    transcript2gene(
      species,
      fasta_file,
      kallisto_out_path,
      type = "vertebrate",
      ...
    )

### Arguments

`species` | A character vector of Latin names of species present in this scRNA-seq dataset. This is used to retrieve Ensembl information from biomart.
`fasta_file` | Character vector of paths to the transcriptome FASTA files used to build the kallisto index. Exactly one of `species` and `fasta_file` can be missing.
`kallisto_out_path` | Path to the `kallisto bus` output directory.
`type` | A character vector indicating the type of each species. Each element must be one of "vertebrate", "metazoa", "plant", "fungus", and "protist". If length is 1, then this type will be used for all species specified here. Can be missing if `fasta_file` is specified.
`...` | Other arguments passed to `tr2g_ensembl` such as `other_attrs`, `ensembl_version`, and arguments passed to `useMart`. If `fasta_files` is supplied instead of `species`, then this will be extra argumennts to `tr2g_fasta`, such as `use_transcript_version` and `use_gene_version`.

### Value

A data frame with two columns: `gene` and `transcript`, with Ensembl gene and transcript IDs (with version number), in the same order as in the transcriptome index used in `kallisto`.

### Note

This function has been superseded by the new version of tr2g_* functions that can extract transcriptome for only the biotypes specified and with only the standard chromosomes. The new version of tr2g_* functions also sorts the transcriptome so the tr2g and the transcriptome have transcripts in the same order.

### See Also

Other functions to retrieve transcript and gene info: `sort_tr2g()`, `tr2g_EnsDb()`, `tr2g_TxDb()`, `tr2g_ensembl()`, `tr2g_fasta()`, `tr2g_gff3()`, `tr2g_gtf()`

### Examples

    # Download dataset already in BUS format
    library(TENxBUSData)
    TENxBUSData(".", dataset = "hgmm100")
    tr2g <- transcript2gene(c("Homo sapiens", "Mus musculus"),
      type = "vertebrate",
      ensembl_version = 99, kallisto_out_path = "./out_hgmm100")

[Package BUSpaRse version 1.4.2 Index]