This data set contains count data for 16S ribosomal RNA (rRNA) sequences for
the two phylogenetic classes Alphaproteobacteria and Mollicutes.
The counts for 30
sequences for each class were obtained by counting the occurrence of triplets
of nucleotides in windows of length 100 without any overlap. To
separate sequences a row of dummy count of NA is used.
Usage
data("16S")Format
Alphaproteobacteria16S and Mollicutes16S are matrices
with about 449 rows and 64 (number of possible triplets) columns.
Source
The raw sequence information was obtained from the National center for biotechnology information (NCBI) website at https://www.ncbi.nlm.nih.gov/
Examples
data("16S")
emm_mollicutes <- EMM("Kullback", threshold=0.1)
emm_alphaproteobacteria <- EMM("Kullback", threshold=0.1)
# build with an added count of 1 for count smoothing
build(emm_mollicutes, Mollicutes16S + 1)
build(emm_alphaproteobacteria, Alphaproteobacteria16S + 1)
plot(emm_mollicutes)
plot(emm_alphaproteobacteria)
