bvseqs {clst} | R Documentation

## BV reference set.

### Description

Tree-derived pairwise distances and taxonomic assignments among 16S rRNA sequences representing bacteria represented in the vaginal mucosa.

### Usage

    data(bvseqs)

### Format

      The format is:
    List of 3
     $ dmat    : num [1:448, 1:448] 0 0.0494 0.0968 0.1002 0.1606 ...
      ..- attr(*, "dimnames")=List of 2
      .. ..$ : chr [1:448] "S001098970" "S000859776" "S000539896" "S001352901" ...
      .. ..$ : chr [1:448] "S001098970" "S000859776" "S000539896" "S001352901" ...
     $ groupTab:'data.frame':	448 obs. of  12 variables:
      ..$ superkingdom    : chr [1:448] "2" "2" "2" "2" ...
      ..$ superphylum     : chr [1:448] NA NA NA NA ...
      ..$ phylum          : chr [1:448] "1224" "1224" "1224" "1224" ...
      ..$ class           : chr [1:448] "1236" "1236" "1236" "1236" ...
      ..$ subclass        : chr [1:448] NA NA NA NA ...
      ..$ order           : chr [1:448] "72274" "72274" "72274" "72274" ...
      ..$ suborder        : chr [1:448] NA NA NA NA ...
      ..$ family          : chr [1:448] "468" "468" "468" "468" ...
      ..$ genus           : chr [1:448] "469" "469" "469" "469" ...
      ..$ species_group   : chr [1:448] NA NA NA NA ...
      ..$ species_subgroup: chr [1:448] NA NA NA NA ...
      ..$ species         : chr [1:448] "470" "470" "471" "470" ...
     $ taxNames: Named chr [1:212] "Actinomyces urogenitalis" "Lactobacillus jensenii" "Proteobacteria" "Gammaproteobacteria" ...
      ..- attr(*, "names")= chr [1:212] "103621" "109790" "1224" "1236" ...

### Details

(Describe creation of this data set)

### Source

Sequences were assembled from both the RDP 16S rRNA database and from the laboratory of Dr. David Fredricks.

### References

RDP url here.

### Examples

    data(bvseqs)
    ## maybe str(bvseqs) ; plot(bvseqs) ...

[Package clst version 1.35.0 Index]