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
- 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)
[[1]]
[[1]][[1]]
[1] 1
[[1]][[2]]
[1] 0
[[2]]
[1] 2
[[3]]
[1] 1