barcode.set.distances: Calculate distances between each barcode pair of a barcode...
In DNABarcodes: A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments

Description Usage Arguments Details Value References See Also Examples

The function calculates the distance between each pair of a set of barcodes. The user may choose one of several distance metrics ("hamming", "seqlev", "levenshtein")).

1	barcode.set.distances(barcodes, metric=c("hamming", "seqlev", "levenshtein"), cores=detectCores()/2, cost_sub = 1, cost_indel = 1)

`barcodes`	A set of barcodes (as vector of characters)
`metric`	The distance metric which should be calculated.
`cores`	The number of cores (CPUs) that will be used for parallel (openMP) calculations.
`cost_sub`	The cost weight given to a substitution.
`cost_indel`	The cost weight given to insertions and deletions.

The primary purpose of this function is the analysis of barcode sets. Seeing the individual paired barcode distances helps to understand which pairings are exceptionally similar and which barcodes have a smaller or higher average distance to other barcodes.

Details if the distance metrics can be found in the man page of create.dnabarcodes.

A symmetric Matrix of distances between each pair of barcodes with zeros on the main diagonal.

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.

analyse.barcodes

1
2
3

barcodes <- c("AGGT", "TTCC", "CTGA", "GCAA")
barcode.set.distances(barcodes)
barcode.set.distances(barcodes,metric="seqlev")

Loading required package: Matrix
Loading required package: parallel
sh: 1: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
4 x 4 Matrix of class "dspMatrix"
     AGGT TTCC CTGA GCAA
AGGT    0    4    3    4
TTCC    4    0    3    4
CTGA    3    3    0    3
GCAA    4    4    3    0
sh: 1: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
4 x 4 Matrix of class "dspMatrix"
     AGGT TTCC CTGA GCAA
AGGT    0    3    3    3
TTCC    3    0    3    3
CTGA    3    3    0    3
GCAA    3    3    3    0