Ensembl2Entrez: Ensembl-to-Entrez gene identifier mappings

Description Usage Arguments Value Note 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

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 2020-01-19.

Examples

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data(RangedSummarizedExperiment, package = "acidtest")
rse <- RangedSummarizedExperiment

## SummarizedExperiment ====
x <- Ensembl2Entrez(rse)
print(x)

acidgenomics/basejump documentation built on Aug. 15, 2020, 10:21 a.m.