mapGeneNamesToEnsembl: Map gene names to Ensembl

In acidgenomics/AcidGenomes: Acid Genomics Genome Annotations

Map gene names to Ensembl

Description

Map gene names to Ensembl

Usage

mapGeneNamesToEnsembl(genes, organism, genomeBuild = NULL, release = NULL)

Arguments

genes	Gene names (e.g. "TUT4").
organism	character(1). Full Latin organism name (e.g. "Homo sapiens").
genomeBuild	character(1). Ensembl genome build assembly name (e.g. "GRCh38"). If set NULL, defaults to the most recent build available. Note: don't pass in UCSC build IDs (e.g. "hg38").
release	integer(1). Ensembl release version (e.g. 100). We recommend setting this value if possible, for improved reproducibility. When left unset, the latest release available via AnnotationHub/ensembldb is used. Note that the latest version available can vary, depending on the versions of AnnotationHub and ensembldb in use.

Details

Internally matches using mapGenesToNCBI first, so we can support gene synonym matching.

Note

Updated 2023-04-14.

Examples

## Homo sapiens.
x <- mapGeneNamesToEnsembl(
    genes = c("TUT4", "ZCCHC11", "TENT3A"),
    organism = "Homo sapiens",
    genomeBuild = "GRCh38",
    release = 109L
)
print(x)

## Mus musculus
x <- mapGeneNamesToEnsembl(
    genes = c("Nfe2l2", "Nrf2"),
    organism = "Mus musculus",
    genomeBuild = "GRCm39",
    release = 109L
)
print(x)

acidgenomics/AcidGenomes documentation built on Dec. 10, 2023, 10:35 p.m.