distance: Calculate distance between two barcodes.

In DNABarcodes: A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments

Description

The function calculates the distance between two barcodes. The user may choose one of several distance metrics ("hamming", "seqlev", "levenshtein", "phaseshift").

Usage

distance(sequence1, sequence2, metric=c("hamming","seqlev","levenshtein", "phaseshift"), cost_sub=1, cost_indel=1) 

Arguments

sequence1	The first sequence (a string)
sequence2	The second sequence (a string)
metric	The distance metric which should be calculated.
cost_sub	The cost weight given to a substitution.
cost_indel	The cost weight given to insertions and deletions.

Value

The distance between the two sequences.

References

Buschmann, T. and Bystrykh, L. V. (2013) Levenshtein error-correcting barcodes for multiplexed DNA sequencing. BMC bioinformatics, 14(1), 272. Available from http://www.biomedcentral.com/1471-2105/14/272.

Levenshtein, V. I. (1966). Binary codes capable of correcting deletions, insertions and reversals. In Soviet physics doklady (Vol. 10, p. 707).

Hamming, R. W. (1950). Error detecting and error correcting codes. Bell System technical journal, 29(2), 147-160.

Examples

distance("AGGT", "TTCC")
distance("AGGT", "TTCC", metric="seqlev")

Example output

Loading required package: Matrix
Loading required package: parallel
[1] 4
[1] 3

DNABarcodes documentation built on Nov. 8, 2020, 5 p.m.