Ensembl-to-Entrez gene identifier mappings

Ensembl2Entrez(object, ...)

Entrez2Ensembl(object, ...)

# S4 method for character
Ensembl2Entrez(object, organism = NULL, format = c("1:1", "long"))

# S4 method for integer
Entrez2Ensembl(object, organism, format = c("1:1", "long"))

# S4 method for GRanges
Ensembl2Entrez(object, format = c("1:1", "long"))

Arguments

object	Object.
...	Additional arguments.
organism	`character(1)`. Full Latin organism name (e.g. `"Homo sapiens"`).
format	`character(1)`. Formatting method to apply: `"1:1"`: Recommended. Return with 1:1 mappings. For Ensembl genes that don't map 1:1 with Entrez, pick the oldest Entrez identifier. Genes that don't map to Entrez will contain `NA` in `entrezId` column. `"long"`: Return 1:many in long format.

Value

Ensembl2Entrez.

Note

Updated 2021-02-24.

Examples

organism <- "Homo sapiens"

## character ====
## Ensembl-to-Entrez.
genes <- c("ENSG00000000003", "ENSG00000000005")
x <- Ensembl2Entrez(object = genes, organism = organism)
#> → Matching identifiers using NCBI `OrgDb` via AnnotationHub 2.22.0.
#> ℹ AH84122 (org.Hs.eg.db.sqlite): NCBI gene ID based annotations about Homo sapiens.
print(x)
#> Ensembl2Entrez with 2 rows and 2 columns
#>                       ensemblId  entrezId
#>                     <character> <integer>
#> ENSG00000000003 ENSG00000000003      7105
#> ENSG00000000005 ENSG00000000005     64102

## integer ====
## Entrez-to-Ensembl.
genes <- c(1L, 2L)
x <- Entrez2Ensembl(object = genes, organism = organism)
#> → Matching identifiers using NCBI `OrgDb` via AnnotationHub 2.22.0.
#> ℹ AH84122 (org.Hs.eg.db.sqlite): NCBI gene ID based annotations about Homo sapiens.
print(x)
#> Entrez2Ensembl with 2 rows and 2 columns
#>    entrezId       ensemblId
#>   <integer>     <character>
#> 1         1 ENSG00000121410
#> 2         2 ENSG00000175899