getMutCount - Determine the mutation counts from allele calls

Description

getMutCount takes a set of nucleotide sequences and their allele calls and determines the distance between that seqeunce and any germline alleles contained within the call

Usage

getMutCount(samples, allele_calls, germline_db)

Arguments

samples
a vector of IMGT-gapped sample V sequences
allele_calls
a vector of strings respresenting Ig allele calls for the sequences in samples, where multiple calls are separated by a comma
germline_db
a vector of named nucleotide germline sequences matching the calls detailed in allele_calls

Value

A list equal in length to samples, containing the Hamming distance to each germline allele contained within each call within each element of samples

Examples

# Load germline database
data(germline_ighv)

# Use createGermlines to insert a mutation into a germline sequence
#sample_seqs = c(germline_ighv[2],
#                createGermlines(germline_ighv[1], 103, "G"),
#                createGermlines(germline_ighv[1], 107, "C"))

# Pretend that one sample sequence has received an ambiguous allele call
#sample_alleles = c(paste(names(germline_ighv[1:2]), collapse=","),
#                  names(germline_ighv[2]),
#                  names(germline_ighv[1]))

# Compare each sequence to its assigned germline(s) to determine the distance
#getMutCount(sample_seqs, sample_alleles, germline_ighv)