R: Calculate pairwise equivalence between sequences

pairwiseEqual {alakazam} | R Documentation

## Calculate pairwise equivalence between sequences

### Description

`pairwiseEqual` determined pairwise equivalence between a pairs in a set of sequences, excluding ambiguous positions (Ns and gaps).

### Usage

    pairwiseEqual(seq)

### Arguments

`seq` | character vector containing a DNA sequences.

### Value

A logical matrix of equivalence between each entry in `seq`. Values are `TRUE` when sequences are equivalent and `FALSE` when they are not.

### See Also

Uses seqEqual for testing equivalence between pairs. See pairwiseDist for generating a sequence distance matrix.

### Examples

    # Gaps and Ns will match any character
    seq <- c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C", E="NTGGG")
    d <- pairwiseEqual(seq)
    rownames(d) <- colnames(d) <- seq
    d

[Package alakazam version 0.3.0 Index]