Ensembl2Entrez: Ensembl-to-Entrez gene identifier mappings

Description Usage Arguments Value Note Examples

Description

Ensembl-to-Entrez gene identifier mappings

Usage

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Ensembl2Entrez(object, ...)

Entrez2Ensembl(object, ...)

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

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

## S4 method for signature 'integer'
Entrez2Ensembl(object, organism, 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 identifier. Genes that don't map to Entrez will contain NA in entrezId column.

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

organism

character(1). Full Latin organism name (e.g. "Homo sapiens").

Value

Ensembl2Entrez.

Note

Updated 2021-08-03.

Examples

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organism <- "Homo sapiens"

## character ====
## Ensembl-to-Entrez.
genes <- c("ENSG00000000003", "ENSG00000000005")
x <- Ensembl2Entrez(object = genes, organism = organism)
print(x)

## integer ====
## Entrez-to-Ensembl.
genes <- c(1L, 2L)
x <- Entrez2Ensembl(object = genes, organism = organism)
print(x)

acidgenomics/AcidGenomes documentation built on Sept. 16, 2021, 7:30 p.m.