dot-checkReferenceAnchor: Checks if mutations and reference genome correspond

In ErasmusMC-CCBC/ProteoDisco: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

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 [e-mail]

Wesley van de Geer [e-mail]

ErasmusMC-CCBC/ProteoDisco documentation built on Dec. 9, 2022, 8:41 a.m.