seqDist | R Documentation |
seqDist
calculates the distance between two DNA sequences.
seqDist(seq1, seq2, dist_mat = getDNAMatrix())
seq1 |
character string containing a DNA sequence. |
seq2 |
character string containing a DNA sequence. |
dist_mat |
Character distance matrix. Defaults to a Hamming distance
matrix returned by getDNAMatrix. If gap
characters, |
Numerical distance between seq1
and seq2
.
Nucleotide distance matrix may be built with getDNAMatrix. Amino acid distance matrix may be built with getAAMatrix. Used by pairwiseDist for generating distance matrices. See seqEqual for testing sequence equivalence.
# Ungapped examples
seqDist("ATGGC", "ATGGG")
seqDist("ATGGC", "ATG??")
# Gaps will be treated as Ns with a gap=0 distance matrix
seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=0))
# Gaps will be treated as universally non-matching characters with gap=1
seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=1))
# Gaps of any length will be treated as single mismatches with a gap=-1 distance matrix
seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))
# Gaps of equivalent run lengths are not counted as gaps
seqDist("ATG-C", "ATG-C", dist_mat=getDNAMatrix(gap=-1))
# Overlapping runs of gap characters are counted as a single gap
seqDist("ATG-C", "AT--C", dist_mat=getDNAMatrix(gap=-1))
seqDist("A-GGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))
seqDist("AT--C", "AT--C", dist_mat=getDNAMatrix(gap=-1))
# Discontiguous runs of gap characters each count as separate gaps
seqDist("-TGGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))
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