seqEqual: Test DNA sequences for equality.

In alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

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")

alakazam documentation built on Sept. 30, 2023, 9:07 a.m.