findUnmutatedCalls - 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
a 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
a vector of named nucleotide germline sequences

Value

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

Examples

# Load data
data(germline_ighv)
data(sample_db)

# Find which of the sample alleles are unmutated
calls <- findUnmutatedCalls(sample_db$V_CALL, sample_db$SEQUENCE_IMGT, 
germline_db=germline_ighv)
head(calls)
[1] "IGHV1-18*01" "IGHV1-69*04" "IGHV1-46*01" "IGHV1-18*01" "IGHV1-18*01" "IGHV1-46*01"