Defines 1:1 mappings from Ensembl gene IDs to Entrez IDs. Uses the oldest Entrez ID if there are multiple identifiers that map to an Ensembl gene ID.

Ensembl2Entrez(object, ...)

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

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

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

Arguments

object

Object.

...

Additional arguments.

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 ID. Genes that don't map to Entrez will contain NA in entrezID column.

  • "long": Return 1:many in long format.

Value

Ensembl2Entrez.

Note

Updated 2019-08-08.

Examples

data(RangedSummarizedExperiment, package = "acidtest") rse <- RangedSummarizedExperiment ## SummarizedExperiment ==== x <- Ensembl2Entrez(rse)
#> 4 genes don't map to Entrez.
#> 2 genes map to multiple Entrez IDs.
#> Returning with 1:1 mappings using oldest Entrez ID per gene.
#> Ensembl2Entrez with 500 rows and 2 columns #> geneID entrezID #> <character> <integer> #> gene001 ENSG00000000003 7105 #> gene002 ENSG00000000005 64102 #> gene003 ENSG00000000419 8813 #> gene004 ENSG00000000457 57147 #> gene005 ENSG00000000460 55732 #> ... ... ... #> gene496 ENSG00000032742 8100 #> gene497 ENSG00000033011 56052 #> gene498 ENSG00000033030 55596 #> gene499 ENSG00000033050 10061 #> gene500 ENSG00000033100 54480