rEMM (version 0.1-2)

16S: Count Data for 16S rRNA Sequences

Description

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 http://www.ncbi.nih.gov/

Examples

data("16S")

emm <- EMM("Kullback", threshold=0.1)
emm <- build(emm, Mollicutes16S+1)

plot(emm, method = "graph")

## start state for sequences have an initial state probability >0
it <- initial_transition(emm)
it[it>0]