nonsquareDist - Calculate pairwise distances between sequences
nonsquareDist calculates all pairwise distance between a set of sequences and a subset of it.
nonsquareDist(seq, indx, dist_mat = getDNAMatrix())
- character vector containing a DNA sequences.
- numeric vector contating the indices (a subset of indices of
- Character distance matrix. Defaults to a Hamming distance
matrix returned by getDNAMatrix. If gap
c("-", "."), are assigned a value of -1 in
dist_matthen contiguous gaps of any run length, which are not present in both sequences, will be counted as a distance of 1. Meaning, indels of any length will increase the sequence distance by 1. Gap values other than -1 will return a distance that does not consider indels as a special case.
A matrix of numerical distance between each entry in
sequences specified by
seq is a named vector, row and columns names will be added
# Gaps will be treated as Ns with a gap=0 distance matrix seq <- c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C") pairwiseDist(seq, dist_mat=getDNAMatrix(gap=0))
A B C D A 0 1 1 0 B 1 0 0 1 C 1 0 0 1 D 0 1 1 0
nonsquareDist(seq, indx=c(1,3), dist_mat=getDNAMatrix(gap=0))
A B C D A 0 1 1 0 C 1 0 0 1