R: Build a DNA distance matrix

getDNAMatrix {alakazam} | R Documentation

## Build a DNA distance matrix

### Description

`getDNAMatrix` returns a Hamming distance matrix for IUPAC ambiguous DNA characters with modifications for gap, `c("-", ".")`, and missing, `c("?")`, character values.

### Usage

    getDNAMatrix(gap = -1)

### Arguments

`gap` | value to assign to characters in the set `c("-", ".")`.

### Value

A `matrix` of DNA character distances with row and column names indicating the character pair. By default, distances will be either 0 (equivalent), 1 (non-equivalent or missing), or -1 (gap).

### See Also

Creates DNA distance matrix for seqDist. See getAAMatrix for amino acid distances.

### Examples

    # Set gap characters to Inf distance
    # Distinguishes gaps from Ns
    getDNAMatrix()

    # Set gap characters to 0 distance
    # Makes gap characters equivalent to Ns
    getDNAMatrix(gap=0)

[Package alakazam version 0.3.0 Index]