utr.annotation (version 1.0.4)

getCodonInAlt: Get the altered codon sequence for transcripts in transcriptIdColumn.

Description

Get the altered codon sequence for transcripts in transcriptIdColumn.

Usage

getCodonInAlt(
  variantsTable,
  transcriptsTable,
  transcriptIdColumn,
  codonPositionsColumn,
  codonSeqColumn
)

Arguments

variantsTable

variants table

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 list containing codon sequences after alt (NA if the transcript id in that row is NA). If transcriptIdColumn, codonPositionsColumn or codonSeqColumn does not exist in the variantsTable, return NA