.checkReferenceAnchor {ProteoDisco}R Documentation

Checks if mutations and reference genome correspond

Description

Overlaps the reference bases and positions with the given genome and check if all positions overlap and reports non-overlapping mutations.

Usage

.checkReferenceAnchor(
  mutations,
  genomeSeqs,
  ignoreNonMatch = FALSE,
  threads = 1
)

Arguments

mutations

(VRanges): Mutations to incorporate within transcripts.

genomeSeqs

(BSgenome or DNAStringSet): Reference genome sequences.

ignoreNonMatch

(logical): Should non-matching reference anchors be ignored? These mutations will be removed.

threads

(integer): Number of threads.

Value

(logical): Returns TRUE/FALSE if per given mutation based on matching position and base with the reference genome.

Author(s)

Job van Riet j.vanriet@erasmusmc.nl

Wesley van de Geer w.vandegeer@erasmusmc.nl


[Package ProteoDisco version 0.99.12 Index]