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

In utr.annotation: Annotate Variants in the Untranslated Regions

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

utr.annotation documentation built on Aug. 23, 2021, 9:06 a.m.