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.
#> 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.
#> 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