tr2g_EnsDb {BUSpaRse} | R Documentation

## Get transcript and gene info from EnsDb objects

### Description

Bioconductor provides Ensembl genome annotation in `AnnotationHub`; older versions of Ensembl annotation can be obtained from packages like `EnsDb.Hsapiens.v86`. This is an alternative to querying Ensembl with biomart; Ensembl's server seems to be less stable than that of Bioconductor. However, more information and species are available on Ensembl biomart than on `AnnotationHub`.

### Usage

    tr2g_EnsDb(
      ensdb,
      other_attrs = NULL,
      use_gene_name = TRUE,
      use_transcript_version = TRUE,
      use_gene_version = TRUE
    )

### Arguments

`ensdb` | Ann `EnsDb` object, such as from `AnnotationHub` or `EnsDb.Hsapiens.v86`.
`other_attrs` | Character vector. Other attributes to get from the `EnsDb` object, such as gene symbol and position on the genome. Use `columns` 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.

### 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_TxDb()`, `tr2g_ensembl()`, `tr2g_fasta()`, `tr2g_gff3()`, `tr2g_gtf()`, `transcript2gene()`

### Examples

    library(EnsDb.Hsapiens.v86)
    tr2g_EnsDb(EnsDb.Hsapiens.v86, use_transcript_version = FALSE,
      use_gene_version = FALSE)

[Package BUSpaRse version 1.1.1 Index]