R: Calculate distance between two sequences

seqDist {alakazam} | R Documentation

## Calculate distance between two sequences

### Description

`seqDist` calculates the distance between two DNA sequences.

### Usage

    seqDist(seq1, seq2, dist_mat = getDNAMatrix())

### Arguments

`seq1` | character string containing a DNA sequence.
`seq2` | character string containing a DNA sequence.
`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

Numerical distance between `seq1` and `seq2`.

### See Also

Nucleotide distance matrix may be built with getDNAMatrix. Amino acid distance matrix may be built with getAAMatrix. Used by pairwiseDist for generating distance matrices. See seqEqual for testing sequence equivalence.

### Examples

    # Ungapped examples
    seqDist("ATGGC", "ATGGG")
    seqDist("ATGGC", "ATG??")

    # Gaps will be treated as Ns with a gap=0 distance matrix
    seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=0))

    # Gaps will be treated as universally non-matching characters with gap=1
    seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=1))

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

    # Gaps of equivalent run lengths are not counted as gaps
    seqDist("ATG-C", "ATG-C", dist_mat=getDNAMatrix(gap=-1))

    # Overlapping runs of gap characters are counted as a single gap
    seqDist("ATG-C", "AT--C", dist_mat=getDNAMatrix(gap=-1))
    seqDist("A-GGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))
    seqDist("AT--C", "AT--C", dist_mat=getDNAMatrix(gap=-1))

    # Discontiguous runs of gap characters each count as separate gaps
    seqDist("-TGGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))

[Package alakazam version 0.3.0 Index]