distance_filter: Select barcode combinations with error correction properties
In comoto-pasteur-fr/DNABarcodeCompatibility: A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms
Description
Usage
Arguments
Details
Value
References
See Also
Examples
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
1
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, 920–922.
See Also
get_all_combinations,
get_random_combinations
Examples
1
2
3
barcodes <- DNABarcodeCompatibility::IlluminaIndexes
m <- get_all_combinations(barcodes, 2, 4)
distance_filter(barcodes, m, "hamming", 3)
comoto-pasteur-fr/DNABarcodeCompatibility documentation built on June 21, 2019, 9:21 a.m.
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Description Usage Arguments Details Value References See Also Examples
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
1 | 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, 920–922.
See Also
get_all_combinations,
get_random_combinations
Examples
1 2 3 | barcodes <- DNABarcodeCompatibility::IlluminaIndexes
m <- get_all_combinations(barcodes, 2, 4)
distance_filter(barcodes, m, "hamming", 3)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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