R: Calculate pairwise distances between sequences

nonsquareDist {alakazam} | R Documentation

## Calculate pairwise distances between sequences

### Description

`nonsquareDist` calculates all pairwise distance between a set of sequences and a subset of it.

### Usage

    nonsquareDist(seq, indx, dist_mat = getDNAMatrix())

### Arguments

`seq` | character vector containing a DNA sequences. The sequence vector needs to be named.
`indx` | numeric vector contating the indices (a subset of indices of `seq`).
`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.

### Value

A matrix of numerical distance between each entry in `seq` and sequences specified by `indx` indices.

Note that the input subsampled indices will be ordered ascendingly. Therefore, it is necassary to assign unique names to the input sequences, `seq`, to recover the input order later. 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.

### Examples

    # 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))

    nonsquareDist(seq, indx=c(1,3),
                 dist_mat=getDNAMatrix(gap=0))

[Package alakazam version 0.3.0 Index]