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Import transcript-to-gene annotations

Source: R/importTxToGene.R
importTxToGene.Rd

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
)
#> → Downloading <https://r.acidgenomics.com/testdata/acidgenomes/tx2gene.csv> to /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/Rtmp4LPYq0/oabYJqFiBj-170173627188968/pipette-feb540536fb6.csv.
#> → Importing <https://r.acidgenomics.com/testdata/acidgenomes/tx2gene.csv> using base::`read.table()`.
print(x)
#> TxToGene with 10 rows and 2 columns
#>                 txId            geneId
#>          <character>       <character>
#> 1  ENST00000415118.1 ENSG00000223997.1
#> 2  ENST00000434970.2 ENSG00000237235.2
#> 3  ENST00000448914.1 ENSG00000228985.1
#> 4  ENST00000631435.1 ENSG00000282253.1
#> 5  ENST00000632524.1 ENSG00000282455.1
#> 6  ENST00000632684.1 ENSG00000282431.1
#> 7  ENST00000632963.1 ENSG00000282674.1
#> 8  ENST00000633009.1 ENSG00000282323.1
#> 9  ENST00000633030.1 ENSG00000282640.1
#> 10 ENST00000634070.1 ENSG00000282724.1