TrainingSet_16S {DECIPHER}R Documentation

Training Set for Classification of 16S rRNA Gene Sequences

Description

A pre-trained classifier for 16S rRNA gene sequences generated by LearnTaxa.

Usage

data("TrainingSet_16S")

Format

A training set of class 'Taxa' * K-mer size: 8 * Number of rank levels: 10 * Total number of sequences: 2472 * Number of taxonomic groups: 2472 * Number of problem groups: 5 * Number of problem sequences: 8

Details

The original training sequences were pruned to a maximum of one sequence per group, as described in the 'Classifying Sequences' vignette.

Note

This 16S rRNA training set is provided for illustrative purposes only. It is highly recommended to use a more comprehensive training set when classifying real sequences. Examples of comprehensive training sets can be found at http://DECIPHER.codes/Download.html.

Source

Derived from version 16 of the RDP Training Set (http://rdp.cme.msu.edu) based on Bergey's Manual.

References

Whitman, W.B., Goodfellow, M., Kampfer, P., Busse, H.-J., Trujillo, M.E., Ludwig, W. & Suzuki, K.-i. (eds., 2012). Bergey's Manual of Systematic Bacteriology, 2nd ed., Springer-Verlag, New York, NY.

Examples

data(TrainingSet_16S)
TrainingSet_16S
plot(TrainingSet_16S)

[Package DECIPHER version 2.14.0 Index]