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"),
      out_path = ".",
      write_tr2g = TRUE,
      other_attrs = NULL,
      use_gene_name = TRUE,
      use_transcript_version = TRUE,
      use_gene_version = TRUE,
      transcript_biotype_col = "transcript_biotype",
      gene_biotype_col = "gene_biotype",
      transcript_biotype_use = "all",
      gene_biotype_use = "all",
      chrs_only = TRUE,
      ensembl_version = NULL,
      overwrite = FALSE,
      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".
`out_path` | Directory to save the outputs written to disk. If this directory does not exist, then it will be created. Defaults to the current working directory.
`write_tr2g` | Logical, whether to write tr2g to disk. If `TRUE`, then a file `tr2g.tsv` will be written into `out_path`.
`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.
`transcript_biotype_col` | Character vector of length 1. Tag in `attribute` field corresponding to transcript biotype.
`gene_biotype_col` | Character vector of length 1. Tag in `attribute` field corresponding to gene biotype.
`transcript_biotype_use` | Character, can be "all" or a vector of transcript biotypes to be used. Transcript biotypes aren't entirely the same as gene biotypes. For instance, in Ensembl annotation, `retained_intron` is a transcript biotype, but not a gene biotype. If "cellranger", then a warning will be given. See `data("ensembl_tx_biotypes")` for all available transcript biotypes from Ensembl.
`gene_biotype_use` | Character, can be "all", "cellranger", or a vector of gene biotypes to be used. If "cellranger", then the biotypes used by Cell Ranger's reference are used. See `data("cellranger_biotypes")` for gene biotypes the Cell Ranger reference uses. See `data("ensembl_gene_biotypes")` for all available gene biotypes from Ensembl. Note that gene biotypes and transcript biotypes are not always the same.
`chrs_only` | Logical, whether to include chromosomes only, for GTF and GFF files can contain annotations for scaffolds, which are not incorporated into chromosomes. This will also exclude haplotypes. Defaults to `TRUE`. Only applicable to species found in `genomeStyles()`.
`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. This only works for vertebrates and the most common invertebrate model organisms like Drosophila melanogaster and C. elegans (i.e. www.ensembl.org and its mirrors), not the other Ensembl sites for plants, protists, fungi, and metazoa.
`overwrite` | Logical, whether to overwrite if files with names of outputs written to disk already exist.
`verbose` | Whether to display progress.
`...` | Othe arguments to be passed to `useMart`, 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

dl_transcriptome

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 = "Danio rerio",
    other_attrs = "description", write_tr2g = FALSE)
    # This will use plants.ensembl.org as host instead of www.ensembl.org
    tr2g <- tr2g_ensembl(species = "Arabidopsis thaliana", type = "plant",
      write_tr2g = FALSE)

[Package BUSpaRse version 1.6.1 Index]