importTxToGene: Import transcript-to-gene annotations

In acidgenomics/AcidGenomes: Acid Genomics Genome Annotations

Import transcript-to-gene annotations

Description

Generates a TxToGene object containing txId and geneId columns.

Usage

importTxToGene(
  file,
  organism = NULL,
  genomeBuild = NULL,
  release = NULL,
  ignoreVersion = c(tx = FALSE, gene = FALSE)
)

Arguments

file	character(1). File path.
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.
ignoreVersion	logical(2). Ignore transcript ("tx") and/or gene ("gene") versions.

Value

TxToGene.

Note

File should not contain column header names.

Updated 2021-02-01.

See Also

• stripTranscriptVersions, stripGeneVersions

Examples

file <- file.path(AcidGenomesTestsUrl, "tx2gene.csv")
x <- importTxToGene(
    file = file,
    organism = "Homo sapiens",
    genomeBuild = "GRCh38",
    release = 100L
)
print(x)

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