Ensembl2Entrez: Ensembl-to-Entrez Gene Identifier Mappings

Description Usage Arguments Value Examples

Description

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.

Usage

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Ensembl2Entrez(object, ...)

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

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

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

Arguments

object

Object.

...

Additional arguments.

format

string. 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. Contains a DataFrame with geneID and entrezID columns.

Examples

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data(rse, package = "basejump.data")
x <- Ensembl2Entrez(rse)
print(x)

steinbaugh/basejump.classes documentation built on Nov. 5, 2018, 10:38 p.m.