utr.annotation (version 1.0.4)

checkIfRefMatchAndAltFragment: Check if the nucleotides in Ref column match the actual nucleotides in the fragment

Description

Check if the nucleotides in Ref column match the actual nucleotides in the fragment

Usage

checkIfRefMatchAndAltFragment(
  fragment,
  fragment_start,
  fragment_end,
  strand,
  ref,
  pos,
  alt,
  refAlwaysFromPlusStrand = TRUE
)

Arguments

fragment

sequence within [fragment_start, fragment_end]

fragment_start

start postion of the fragment

fragment_end

end postion of the fragment

strand

strand of the current sequence, 1 or -1

ref

nucleotides in Ref column

pos

variant postion in Pos column

alt

nucleotides in Alt column

Value

ragment sequence after mutation or -1 if the nucleotides in Ref column do not match the actual nucleotides in the sequence