R: Test DNA sequences for equality.

seqEqual {alakazam} | R Documentation

## Test DNA sequences for equality.

### Description

`seqEqual` checks if two DNA sequences are identical.

### Usage

    seqEqual(seq1, seq2, ignore = as.character(c("N", "-", ".", "?")))

### Arguments

`seq1` | character string containing a DNA sequence.
`seq2` | character string containing a DNA sequence.
`ignore` | vector of characters to ignore when testing for equality. Default is to ignore c("N",".","-","?")

### Value

Returns `TRUE` if sequences are equal and `FALSE` if they are not. Sequences of unequal length will always return `FALSE` regardless of their character values.

### See Also

Used by pairwiseEqual within collapseDuplicates. See seqDist for calculation Hamming distances between sequences.

### Examples

    # Ignore gaps
    seqEqual("ATG-C", "AT--C")
    seqEqual("ATGGC", "ATGGN")
    seqEqual("AT--T", "ATGGC")

    # Ignore only Ns
    seqEqual("ATG-C", "AT--C", ignore="N")
    seqEqual("ATGGC", "ATGGN", ignore="N")
    seqEqual("AT--T", "ATGGC", ignore="N")

[Package alakazam version 0.3.0 Index]