getTranscriptSequence: getTranscriptSequence

In ETHZ-INS/scanMiRApp: scanMiR shiny application

getTranscriptSequence

Description

Utility wrapper to extracts the sequence of a given transcript (UTR or CDS+UTR).

Usage

getTranscriptSequence(
  tx = NULL,
  annotation,
  annoFilter = NULL,
  extract = c("UTRonly", "withORF", "exons"),
  ...
)

Arguments

tx	The ensembl ID of the transcript(s)
annotation	A ScanMiRAnno object.
annoFilter	An optional 'AnnotationFilter' or 'AnnotationFilterList' to further filter the set of transcripts to be extracted
extract	Which parts of the transcripts to extract. For 'UTRonly' (default) only the 3' UTR regions are extracted, 'withORF' additionally extracts the coding regions, and 'exons' extracts all exons
...	Passed to AnnotationHub

Value

A DNAStringSet.

Examples

anno <- ScanMiRAnno("fake")
seq <- getTranscriptSequence( tx="ENSTFAKE0000056456", annotation=anno )

ETHZ-INS/scanMiRApp documentation built on March 16, 2024, 5:30 p.m.