utr.annotation (version 1.0.4)

checkIfLostCodonAfterAltOneVariant: Check if the codon lost after alt for one variant.

Description

Check if the codon lost after alt for one variant.

Usage

checkIfLostCodonAfterAltOneVariant(variant, colNameAfterAlt, patterns)

Arguments

variant

variant info

colNameAfterAlt

the name of the codon column after alter, type of a string. For example, name of column for the stop codon sequence after alt

patterns

codon patterns, "ATG" for start codon, c("TAG", "TAA", "TGA") for stop codon

Value

A string concatenated TURE or FALSE or NA of all transcripts for that variant. If colNameAfterAlt is NA, return NA