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.

Note

Updated 2023-07-31.

GFF/GTF file

Remote URLs and compressed files are supported.

Examples

## makeTxToGeneFromEnsembl ====
x <- makeTxToGeneFromEnsembl(organism = "Homo sapiens")
#> → Making <GRanges> from Ensembl.
#> → Getting <EnsDb> from AnnotationHub 3.10.0 (2023-10-20).
#> ℹ "AH113665": Ensembl 110 EnsDb for Homo sapiens.
#> → Making <GRanges> from <EnsDb>.
#> Organism: Homo sapiens
#> Genome build: GRCh38
#> Release: 110
#> Level: transcripts
#> → Defining names by `txId` column in `mcols()`.
print(x)
#> TxToGene with 278545 rows and 2 columns
#>                                  txId             geneId
#>                           <character>        <character>
#> ENST00000000233.10 ENST00000000233.10 ENSG00000004059.11
#> ENST00000000412.8   ENST00000000412.8  ENSG00000003056.8
#> ENST00000000442.11 ENST00000000442.11 ENSG00000173153.17
#> ENST00000001008.6   ENST00000001008.6  ENSG00000004478.8
#> ENST00000001146.7   ENST00000001146.7  ENSG00000003137.9
#> ...                               ...                ...
#> LRG_998t2.1               LRG_998t2.1          LRG_998.1
#> LRG_999t1.1               LRG_999t1.1          LRG_999.1
#> LRG_999t2.1               LRG_999t2.1          LRG_999.1
#> LRG_99t1.1                 LRG_99t1.1           LRG_99.1
#> LRG_9t1.1                   LRG_9t1.1            LRG_9.1

## 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)