Strip transcript identifier versions

stripGeneVersions(object, ...)

stripTranscriptVersions(object, ...)

# S4 method for SummarizedExperiment
stripGeneVersions(object)

# S4 method for SummarizedExperiment
stripTranscriptVersions(object)

Arguments

object

Object.

...

Additional arguments.

Value

Modified object. Contains transcript identifiers without version numbers.

Details

Intentionally does not strip gene versions, if defined in the object. To perform that action in parallel, use stripVersions instead.

Note

Updated 2021-02-03.

See also

  • http://www.ensembl.org/info/genome/stable_ids/index.html

Examples

data(SummarizedExperiment_transcripts, package = "AcidTest") rowData <- SummarizedExperiment::rowData ## SummarizedExperiment ==== object <- SummarizedExperiment_transcripts head(rowData(object)[["txId"]])
#> [1] "ENST00000494424.1" "ENST00000496771.5" "ENST00000612152.4" #> [4] "ENST00000371584.8" "ENST00000371588.9" "ENST00000413082.1"
head(rowData(object)[["geneId"]])
#> [1] "ENSG00000000003.15" "ENSG00000000003.15" "ENSG00000000003.15" #> [4] "ENSG00000000419.12" "ENSG00000000419.12" "ENSG00000000419.12"
head(rownames(object))
#> [1] "ENST00000494424.1" "ENST00000496771.5" "ENST00000612152.4" #> [4] "ENST00000371584.8" "ENST00000371588.9" "ENST00000413082.1"
object <- stripGeneVersions(object)
#> ! No gene versions to modify.
object <- stripTranscriptVersions(object) head(rowData(object)[["txId"]])
#> [1] "ENST00000494424.1" "ENST00000496771.5" "ENST00000612152.4" #> [4] "ENST00000371584.8" "ENST00000371588.9" "ENST00000413082.1"
head(rowData(object)[["geneId"]])
#> [1] "ENSG00000000003.15" "ENSG00000000003.15" "ENSG00000000003.15" #> [4] "ENSG00000000419.12" "ENSG00000000419.12" "ENSG00000000419.12"
head(rownames(object))
#> [1] "ENST00000494424" "ENST00000496771" "ENST00000612152" "ENST00000371584" #> [5] "ENST00000371588" "ENST00000413082"