R: Determine the mutation counts from allele calls

getMutCount {tigger} | R Documentation

## 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` | 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`

### 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

    # 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)

[Package tigger version 1.0.0 Index]