Generate the transition matrix from the original DNA methylation level to the terminal DNA methylation level which is suitable for TMParameterEstimation().
The original methylation level of each CpG/gene/region.
The paired terminal methylation level of each CpG/gene/region.
observation_matrix The transition ratio matrix(5 \times 5) from the original state to the terminal state. DNA methylation level was classed to five classes (class1:0;class1:1/4;class1:1/2;class1:3/4;class5:1). The ratio of each class change to others are described as blows:
# observation_matrix[1,1](a1) is the ratio of original_class1 to terminal_class1,observation_matrix[1,2](b1) is the ratio of original_class2 to terminal_class1 and so on # observation_matrix[2,1](a2) is the ratio of original_class1 to terminal_class2,observation_matrix[2,2](b2) is the ratio of original_class2 to terminal_class2 and so on # The sum of the ratio that original_class1 change to 5 classes should be 1. That is a1+a2+a3+a4+a5=1.
Zhao, C. et.al.(2019). A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in pre-implantation embryos. Under revision.
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