TrainingSet_16S: Training Set for Classification of 16S rRNA Gene Sequences

In DECIPHER: Tools for curating, analyzing, and manipulating biological 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)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

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

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.