alakazam (version 1.3.0)

pairwiseDist: Calculate pairwise distances between sequences

Description

pairwiseDist calculates all pairwise distance between a set of sequences.

Usage

pairwiseDist(seq, dist_mat = getDNAMatrix())

Value

A matrix of numerical distance between each entry in seq. If seq is a named vector, row and columns names will be added accordingly.

Amino acid distance matrix may be built with getAAMatrix. Uses seqDist for calculating distances between pairs. See pairwiseEqual for generating an equivalence matrix.

Arguments

seq

character vector containing a DNA sequences.

dist_mat

Character distance matrix. Defaults to a Hamming distance matrix returned by getDNAMatrix. If gap characters, c("-", "."), are assigned a value of -1 in dist_mat then 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.

Examples

# Gaps will be treated as Ns with a gap=0 distance matrix
pairwiseDist(c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C"), 
             dist_mat=getDNAMatrix(gap=0))

# Gaps will be treated as universally non-matching characters with gap=1
pairwiseDist(c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C"), 
             dist_mat=getDNAMatrix(gap=1))

# Gaps of any length will be treated as single mismatches with a gap=-1 distance matrix
pairwiseDist(c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C"), 
             dist_mat=getDNAMatrix(gap=-1))