utr.annotation (version 1.0.4)

getCodonInAltOneVariant: Get the altered codon sequence for transcripts in transcriptIdColumn for one variant.

Description

Get the altered codon sequence for transcripts in transcriptIdColumn for one variant.

Usage

getCodonInAltOneVariant(
  variant,
  transcriptsTable,
  transcriptIdColumn,
  codonPositionsColumn,
  codonSeqColumn
)

Arguments

variant

variant info

transcriptIdColumn

the name of the transcript id column for the codon region

codonSeqColumn

the codon sequence column output from getCodon

trascriptsTable

transcripts structure table from ensembl with start and end columns for start and end coordinates of the target regions

codonPositionsColumnn

the codon coordinates column output from getTranscriptIdsForCodonVariants

Value

A string concatenated codon sequences after alt (NA if the transcript id in that row is NA).