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 |
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 |
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
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")