R: Obtain gene symbols for entrezgene IDs

entrez_to_symbol {dnapath} | R Documentation

## Obtain gene symbols for entrezgene IDs

### Description

Uses `biomaRt` (Durinck et al. 2009) to map entrezgene IDs to gene symbols for a given species. Obtains MGI symbols for mouse species and HGNC symbols for other species. (Note: this mapping may not work for all species.) The output of this function can be used in `rename_genes`.

### Usage

    entrez_to_symbol(
      x,
      species,
      symbol_name = NULL,
      dir_save = tempdir(),
      verbose = TRUE
    )

### Arguments

`x` | A vector of entrezgene IDs.
`species` | The species used to obtain the entrezgene IDs. For example: "Homo sapiens", "m musculus", "C. elegans", or "S cerevisiae". "Human" and "mouse" can also be used and will be converted to the correct species name.
`symbol_name` | The type of gene symbol to use. If NULL, then "hgnc_symbol" is used for HGNC symbols, unless `species` is "mmusculus", in which case
`dir_save` | The directory to store annotation reference. Future calls to this function will use the stored annotations. This speeds up the operation and allows for reproducibility in the event that the `biomaRt` database is updated. Set to NULL to disable. By default, it uses a temporary directory to store files during the R session. "mgi_symbol" is used.
`verbose` | Set to FALSE to avoid messages.

### Details

If entrezgene IDs are used in a `dnapath_list` or `dnapath` object, or a pathway list, then `get_genes` can be used to extract them and used for the `x` argument here.

### Value

A data frame with two columns: the first contains the original entrezgene IDs, and the second contains the corresponding gene symbols. MGI symbols are returned when `species = "Mus musculus"` and HGNC symbols are returned otherwise.

### Note

Internet connection is required to connect to biomaRt. If unavailable, the default biomart and default species contained in the package is used, but this may not match the desired species.

### References

Durinck S, Spellman PT, Birney E, Huber W (2009). “Mapping Identifiers for the Integration of Genomic Datasets with the R/Bioconductor Package biomaRt.” Nature Protocols, 4, 1184–1191.

### See Also

`symbol_to_entrez`, `get_genes`

### Examples

    data(meso)
    # The meso gene expression data contains entrezgene IDs.
    # These can be converted to gene symbols.
    gene_mat <- entrez_to_symbol(colnames(meso$gene_expression), species = "human")

[Package dnapath version 0.7.4 Index]