diff --git a/docs/src/getstarted.md b/docs/src/getstarted.md index 1bf6470..f9ac517 100644 --- a/docs/src/getstarted.md +++ b/docs/src/getstarted.md @@ -20,15 +20,16 @@ seq = dna"CCTCCCGGACCCTGGGCTCGGGAC" BioMarkovChain(sequence) ``` - - BioMarkovChain of DNAAlphabet{4}() and order 1: - - Transition Probability Matrix -> Matrix{Float64}(4 × 4): - 0.0 1.0 0.0 0.0 - 0.0 0.5 0.2 0.3 - 0.25 0.125 0.625 0.0 - 0.0 0.6667 0.3333 0.0 - - Initial Probabilities -> Vector{Float64}(4 × 1): - 0.087 0.4348 0.3478 0.1304 +``` +BioMarkovChain of DNAAlphabet{4}() and order 1: + - Transition Probability Matrix -> Matrix{Float64}(4 × 4): + 0.0 1.0 0.0 0.0 + 0.0 0.5 0.2 0.3 + 0.25 0.125 0.625 0.0 + 0.0 0.6667 0.3333 0.0 + - Initial Probabilities -> Vector{Float64}(4 × 1): + 0.087 0.4348 0.3478 0.1304 +``` Note that, sometimes the dinucleotides transition do not harbor important biological meaning, whereas trinucleotides or codons are, in fact, the building block of proteins. Therefore, sometimes the transition model we want to build is usually a second-order Markov chain, that represents the possible transitions of a trinucleotide. @@ -38,12 +39,13 @@ A very nice nice property of the transition probability matrix is that the *n-st ``` julia BioMarkovChain(sequence, 2) ``` - - BioMarkovChain of DNAAlphabet{4}() and order 2: - - Transition Probability Matrix -> Matrix{Float64}(4 × 4): - 0.0 0.5 0.2 0.3 - 0.05 0.475 0.325 0.15 - 0.1562 0.3906 0.4156 0.0375 - 0.0833 0.375 0.3417 0.2 - - Initial Probabilities -> Vector{Float64}(4 × 1): - 0.087 0.4348 0.3478 0.1304 \ No newline at end of file +``` +BioMarkovChain of DNAAlphabet{4}() and order 2: + - Transition Probability Matrix -> Matrix{Float64}(4 × 4): + 0.0 0.5 0.2 0.3 + 0.05 0.475 0.325 0.15 + 0.1562 0.3906 0.4156 0.0375 + 0.0833 0.375 0.3417 0.2 + - Initial Probabilities -> Vector{Float64}(4 × 1): + 0.087 0.4348 0.3478 0.1304 +``` \ No newline at end of file