distance_filter: Select barcode combinations with error correction properties

In DNABarcodeCompatibility: A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms

Description

Filters a list of barcode combinations for a given distance metric (hamming or seqlev) and threshold in order to produce a list of barcodes satisfying the distance constraints.

Usage

distance_filter(index_df, combinations_m, metric, d)

Arguments

index_df	A dataframe containing barcodes identifiers, corresponding DNA sequences along with GC content and presence of homopolymers.
combinations_m	A matrix of compatible barcode combinations.
metric	The type of distance (hamming or seqlev or phaseshift).
d	The minimum value of the distance.

Details

The "hamming" distance is suitable for correcting substitution errors. The "seqlev" distance is suitable for correcting both substitution and insertion/deletion errors.

Value

A filtered matrix containing the identifiers of the barcodes satisfying the distance constraints.

References

Buschmann, T. 2015. The Systematic Design and Application of Robust DNA Barcodes.

Buschmann, T. 2017. DNABarcodes: an R package for the systematic construction of DNA sample tags. Bioinformatics 33, 920<e2><80><93>922.

See Also

get_all_combinations, get_random_combinations

Examples

barcodes <- DNABarcodeCompatibility::IlluminaIndexes
m <- get_all_combinations(barcodes, 2, 4)
distance_filter(barcodes, m, "hamming", 3)

DNABarcodeCompatibility documentation built on Nov. 8, 2020, 5:36 p.m.