tr2g_ensembl {BUSpaRse} | R Documentation

## Get transcript and gene info from Ensembl

### Description

This function queries Ensembl biomart to convert transcript IDs to gene IDs.

### Usage

    tr2g_ensembl(
      species,
      type = c("vertebrate", "metazoa", "plant", "fungus", "protist"),
      other_attrs = NULL,
      use_gene_name = TRUE,
      use_transcript_version = TRUE,
      use_gene_version = TRUE,
      ensembl_version = NULL,
      verbose = TRUE,
      ...
    )

### Arguments

`species` | Character vector of length 1, Latin name of the species of interest.
`type` | Character, must be one of "vertebrate", "metazoa", "plant", "fungus" and "protist". Passing "vertebrate" will use the default www.ensembl.org host. Gene annotation of some common invertebrate model organisms, such as Drosophila melanogaster, are available on www.ensembl.org so for these invertebrate model organisms, "vertebrate" can be used for this argument. Passing values other than "vertebrate" will use other Ensembl hosts. For animals absent from www.ensembl.org, try "metazoa".
`other_attrs` | Character vector. Other attributes to get from Ensembl, such as gene symbol and position on the genome. Use `listAttributes` to see which attributes are available.
`use_gene_name` | Logical, whether to get gene names.
`use_transcript_version` | Logical, whether to include version number in the Ensembl transcript ID. To decide whether to include transcript version number, check whether version numbers are included in the `transcripts.txt` in the `kallisto` output directory. If that file includes version numbers, then trannscript version numbers must be included here as well. If that file does not include version numbers, then transcript version numbers must not be included here.
`use_gene_version` | Logical, whether to include version number in the Ensembl gene ID. Unlike transcript version number, it's up to you whether to include gene version number.
`ensembl_version` | Integer version number of Ensembl (e.g. 94 for the October 2018 release). This argument defaults to `NULL`, which will use the current release of Ensembl. Use `listEnsemblArchives` to see the version number corresponding to the Ensembl release of a particular date. The version specified here must match the version of Ensembl where the transcriptome used to build the kallisto index was downloaded.
`verbose` | Whether to display progress.
`...` | Othe arguments to be passed to `useEnsembl`, such as mirror. Note that setting mirrors other than the default, e.g. uswest, does not work for archived versions.

### Value

A data frame with at least 2 columns: `gene` for gene ID, `transcript` for transcript ID, and optionally `gene_name` for gene names. If `other_attrs` has been specified, then those will also be columns in the data frame returned.

### See Also

Other functions to retrieve transcript and gene info: `sort_tr2g()`, `tr2g_EnsDb()`, `tr2g_TxDb()`, `tr2g_fasta()`, `tr2g_gff3()`, `tr2g_gtf()`, `transcript2gene()`

### Examples

    tr2g <- tr2g_ensembl(species = "Felis catus", other_attrs = "description")
    # This will use plants.ensembl.org as host instead of www.ensembl.org
    tr2g <- tr2g_ensembl(species = "Arabidopsis thaliana", type = "plant")

[Package BUSpaRse version 1.1.1 Index]