tigger (version 1.1.0)

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)

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

Arguments

samples

vector of IMGT-gapped sample V sequences

allele_calls

vector of strings respresenting Ig allele calls for the sequences in samples, where multiple calls are separated by a comma

germline_db

vector of named nucleotide germline sequences matching the calls detailed in allele_calls

Examples

# Insert a mutation into a germline sequence
s2 <- s3 <- SampleGermlineIGHV[1]
stringi::stri_sub(s2, 103, 103) <- "G"
stringi::stri_sub(s3, 107, 107) <- "C"

sample_seqs <- c(SampleGermlineIGHV[2], s2, s3)

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

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