Generates a Tx2Gene object containing transcriptID and geneID columns.

importTx2Gene(file, organism = NULL, genomeBuild = NULL,
  ensemblRelease = NULL)

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").

ensemblRelease

integer(1). Ensembl release version (e.g. 90). 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.

Value

Tx2Gene.

Note

File should not contain column header names.

The functon doesn't attempt to strip transcript versions. Use stripTranscriptVersions() in a separate call, if necessary.

Updated 2019-10-24.

Examples

file <- file.path(basejumpTestsURL, "tx2gene.csv") x <- importTx2Gene( file = file, organism = "Mus musculus", genomeBuild = "GRCm38", ensemblRelease = 90L )
#> Importing 'tx2gene.csv' using 'data.table::fread()'.
#> Tx2Gene with 5 rows and 2 columns #> transcriptID geneID #> <character> <character> #> 1 ENSMUST00000033908 ENSMUSG00000031511 #> 2 ENSMUST00000070080 ENSMUSG00000056124 #> 3 ENSMUST00000119854 ENSMUSG00000037736 #> 4 ENSMUST00000174016 ENSMUSG00000036036 #> 5 ENSMUST00000204196 ENSMUSG00000029804