inFrameFusions: Evaluates whether a rearranged DNA sequence is in-frame

In cancer-genomics/trellis: Somatic structural variant analysis

Evaluates whether a rearranged DNA sequence is in-frame

Description

A rearranged sequence is considered in-frame if the protein sequence derived from the DNA sequence 3-prime of the new sequence junction is a subset of the reference protein sequence.

Usage

inFrameFusions(fused.proteins, ref.protein, fused.txlist)

Arguments

fused.proteins	the rearranged protein sequence
ref.protein	the unrearranged (reference) protein sequence
fused.txlist	a GRangesList of the fused transcripts

See Also

See referenceProtein and tumorProtein for extracting the unrearranged and rearranged protein sequences, respectively. See clip and fuse for extracting the fused, clipped transcript sequence as a GRangesList object. See fullTranscripts for extracting the full transcripts as a GRangesList.

Examples

  library(BSgenome.Hsapiens.UCSC.hg19)
  genome <- BSgenome.Hsapiens.UCSC.hg19
  data(rear_cds, package="trellis")
  unrear_cds <- fullTranscripts(rear_cds)
  ##
  ## referenceProtein
  ##
  ref_protein <- referenceProtein(genome, unrear_cds, names(unrear_cds))
  fused_tx <- fuse(clip(rear_cds))
  fused_protein <- tumorProtein(genome, fused_tx)
  inFrameFusions(fused_protein, ref_protein, fused_tx)

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.