analyse.barcodes: Analyse Sets of Barcode

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

Description

The function analyses the properties of sets of (potential) barcodes. For various metrics, minimal, maximal and average distances are calculated and hints on error correction capabilities of the code are given.

Usage

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

Arguments

barcodes	A vector of characters that represent the barcodes. All barcodes must be of equal length and consist only of letters A, C, G, and T. Lower case letters are allowed but do not make a difference.
metric	A vector of one or more metric names whose distances shall be calculated for the barcode set. Default is to use all of them.
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.

Value

A data frame of properties of the barcode set with the following meanings:

Columns: The first column contains a description of the barcode set properties. Each next column names the metric.

Rows: "Mean Distance", "Median Distance", "Minimum Distance", "Maximum Distance", "Guaranteed Error Correction", "Guaranteed Error Detection"

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.

See Also

barcode.set.distances

Examples

barcodes <- c("ACG", "CGT", "TGC")
analyse.barcodes(barcodes)

##
##                 Description  hamming   seqlev levenshtein
##               Mean Distance 2.666667 1.666667    2.333333
##             Median Distance 3.000000 2.000000    2.000000
##            Minimum Distance 2.000000 1.000000    2.000000
##            Maximum Distance 3.000000 2.000000    3.000000
## Guaranteed Error Correction 0.000000 0.000000    0.000000
##  Guaranteed Error Detection 1.000000 0.000000    1.000000

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