getTranscriptSequence: getTranscriptSequence

Description Usage Arguments Value Examples

View source: R/getTranscriptSequence.R

Description

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

Usage

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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

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

ETHZ-INS/scanMiRApp documentation built on Jan. 20, 2022, 5:51 p.m.