16S: Count Data for 16S rRNA Sequences
In rEMM: Extensible Markov Model for Modelling Temporal Relationships Between Clusters
16S R Documentation
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)
build(emm, Mollicutes16S+1)
## start state for sequences have an initial state probability >0
it <- initial_transition(emm)
it[it>0]
rEMM documentation built on June 26, 2022, 1:06 a.m.
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| 16S | R Documentation |
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)
build(emm, Mollicutes16S+1)
## start state for sequences have an initial state probability >0
it <- initial_transition(emm)
it[it>0]
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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