Build kmer database for classifying 16S rRNA and other gene sequences to a genus when a kmer size is provided.
Arguments
- sequences
A vector of reference sequences for which we have genus-level taxonomic information in the same order as the value for genera.
- genera
A character vector of genus-level taxonomic information for reference sequences in the same order as the value for sequences. Ideally, taxonomic information will be provided back to the domain level with each level separated by semicolons and no spaces.
- kmer_size
An integer indicating the length of the nucleotide word to base our classification on (default = 8)
Value
A list object containing the genus level conditional probability
(conditional_prob) of seeing each kmer in a given genus as well as
the genus names (genera)
References
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 Aug;73(16):5261-7. doi:10.1128/AEM.00062-07 PMID: 17586664; PMCID: PMC1950982.
Examples
kmer_size <- 3
sequences <- c("ATGCGCTA", "ATGCGCTC", "ATGCGCTC")
genera <- c("A", "B", "B")
build_kmer_database(sequences, genera, kmer_size)
#> $conditional_prob
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7]
#> [1,] -2.772589 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589
#> [2,] -3.178054 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054
#> [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> [1,] -2.772589 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589
#> [2,] -3.178054 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054
#> [,15] [,16] [,17] [,18] [,19] [,20] [,21]
#> [1,] -0.06453852 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589
#> [2,] -0.04255961 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054
#> [,22] [,23] [,24] [,25] [,26] [,27] [,28]
#> [1,] -2.772589 -2.772589 -2.772589 -2.772589 -0.06453852 -2.772589 -2.772589
#> [2,] -3.178054 -3.178054 -3.178054 -3.178054 -0.04255961 -3.178054 -3.178054
#> [,29] [,30] [,31] [,32] [,33] [,34] [,35]
#> [1,] -0.3746934 -1.1631508 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589
#> [2,] -2.0794415 -0.1335314 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054
#> [,36] [,37] [,38] [,39] [,40] [,41] [,42]
#> [1,] -2.772589 -2.772589 -2.772589 -0.06453852 -0.06453852 -2.772589 -2.772589
#> [2,] -3.178054 -3.178054 -3.178054 -0.04255961 -0.04255961 -3.178054 -3.178054
#> [,43] [,44] [,45] [,46] [,47] [,48] [,49]
#> [1,] -2.772589 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589
#> [2,] -3.178054 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054
#> [,50] [,51] [,52] [,53] [,54] [,55] [,56]
#> [1,] -2.772589 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589
#> [2,] -3.178054 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054
#> [,57] [,58] [,59] [,60] [,61] [,62] [,63]
#> [1,] -2.772589 -0.06453852 -2.772589 -2.772589 -2.772589 -2.772589 -2.772589
#> [2,] -3.178054 -0.04255961 -3.178054 -3.178054 -3.178054 -3.178054 -3.178054
#> [,64]
#> [1,] -2.772589
#> [2,] -3.178054
#>
#> $genera
#> [1] "A" "B"
#>