findUnmutatedCalls: Determine which calls represent an unmutated allele

In tigger: Infers Novel Immunoglobulin Alleles from Sequencing Data

Determine which calls represent an unmutated allele

Description

findUnmutatedCalls determines which allele calls would represent a perfect match with the germline sequence, given a vector of allele calls and mutation counts. In the case of multiple alleles being assigned to a sequence, only the subset that would represent a perfect match is returned.

Usage

findUnmutatedCalls(allele_calls, sample_seqs, germline_db)

Arguments

allele_calls	vector of strings respresenting Ig allele calls, where multiple calls are separated by a comma.
sample_seqs	V(D)J-rearranged sample sequences matching the order of the given allele_calls.
germline_db	vector of named nucleotide germline sequences

Value

A vector of strings containing the members of allele_calls that represent unmutated sequences.

Examples

# Find which of the sample alleles are unmutated
calls <- findUnmutatedCalls(AIRRDb$v_call, AIRRDb$sequence_alignment, 
                            germline_db=SampleGermlineIGHV)

tigger documentation built on Oct. 10, 2023, 5:08 p.m.