makeTxToGene: Make a TxToGene object

In acidgenomics/AcidGenomes: Acid Genomics Genome Annotations

Make a TxToGene object

Description

Make a TxToGene object

Usage

makeTxToGeneFromEnsembl(
  organism,
  genomeBuild = NULL,
  release = NULL,
  ignoreVersion = FALSE
)

makeTxToGeneFromEnsDb(object, ignoreVersion = FALSE)

makeTxToGeneFromGff(file, ignoreVersion = FALSE)

Arguments

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(1). Ignore identifier (e.g. transcript, gene) versions. When applicable, the identifier containing version numbers will be stored in txIdVersion and geneIdVersion, and the variants without versions will be stored in txId, txIdNoVersion, geneId, and geneIdNoVersion.
object	Object.
file	character(1). File path.

Value

TxToGene.

GFF/GTF file

Remote URLs and compressed files are supported.

Note

Updated 2023-07-31.

Examples

## makeTxToGeneFromEnsembl ====
x <- makeTxToGeneFromEnsembl(organism = "Homo sapiens")
print(x)

## makeTxToGeneFromEnsDb ====
## > if (goalie::isInstalled("EnsDb.Hsapiens.v75")) {
## >     x <- makeTxToGeneFromEnsDb(object = "EnsDb.Hsapiens.v75")
## >     print(x)
## > }

## makeTxToGeneFromGff ====
## > file <- AcidBase::pasteUrl(
## >     "ftp.ensembl.org",
## >     "pub",
## >     "release-102",
## >     "gtf",
## >     "homo_sapiens",
## >     "Homo_sapiens.GRCh38.102.gtf.gz",
## >     protocol = "ftp"
## > )
## > x <- makeTxToGeneFromGff(file = file)
## > print(x)

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