Randomly generate a 4 X 4 stochastic matrix that satisfies Chargaff's second parity rule for dinucleotides.
rcspr2mat(labels=c("a", "c", "g", "t"))A 4 X 4 stochastic matrix satisfying Chargaff's second parity rule. The rows and columns are labelled according to labels.
a vector of labels for the rows and columns of the matrix. By default, this is set to the set of four nucleotides a, c, g and t.
Andrew Hart and Servet Martínez
This function randomly generates Stochastic matrices of the form
$$ \left(\begin{array}{cccc} b_1&b_2&b_3&1-(b_1+b_2+b_3) \\ zb_6&b_4 & 1-(zb_6+b_4+zb_3) & zb_3 \\ zb_5 &1-(zb_5+b_4+zb_2) & b_4&zb_2 \\ 1-(b_5+b_6+b_1)&b_5&b_6&b_1 \end{array}\right) $$
where \(b_1\), ..., \(b_6\) are values in the interval (0,1) and \(z\) is a positive number.
Such matrices characterize sequences of DNA that comply with Chargaff's second parity rule for dinucleotides. See the reference for further information.
Hart, A.G. and Martínez, S. (2011) Statistical testing of Chargaff's second parity rule in bacterial genome sequences. Stoch. Models 27(2), 1--46.
rstochmat