seqEqual - 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.

Examples¶

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

[1] TRUE

seqEqual("ATGGC", "ATGGN")

[1] TRUE

seqEqual("AT--T", "ATGGC")

[1] FALSE

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

[1] FALSE

seqEqual("ATGGC", "ATGGN", ignore="N")

[1] TRUE

seqEqual("AT--T", "ATGGC", ignore="N")

[1] FALSE

See also¶

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