bvseqs: BV reference set.

In clst: Classification by local similarity threshold

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) ...

clst documentation built on Nov. 8, 2020, 5:41 p.m.