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

In utr.annotation: Annotate Variants in the Untranslated Regions

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

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