TransitionMatrixGeneration: "TransitionMatrixGeneration"

In ChengchenZhao/MethylTransition: Estimated DNA Methylation Parameters and Calculate Methylation Classes after n Cell Cycle(s)

Description

Generate the transition matrix from the original DNA methylation level to the terminal DNA methylation level which is suitable for TMParameterEstimation().

Usage

TransitionMatrixGeneration(original_methyl, terminal_methyl)

Arguments

original_methyl	The original methylation level of each CpG/gene/region.
terminal_methyl	The paired terminal methylation level of each CpG/gene/region.

Details

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Value

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:

	original_class1	original_class2	original_class3	original_class4	original_class5
terminal_class1	a1	b1	c1	d1	e1
terminal_class2	a2	b2	c2	d2	e2
terminal_class3	a3	b3	c3	d3	e3
terminal_class4	a4	b4	c4	d4	e4
terminal_class5	a5	b5	c5	d5	e5

# 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.

References

Zhao, C. et.al.(2019). A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in pre-implantation embryos. Under revision.

Examples

# Let's simulate the original DNA methylation level vector and the terminal one.
set.seed(0)
original_methyl <- runif(10000, min = 0, max = 1)
set.seed(1)
terminal_methyl <- runif(10000, min = 0, max = 1)
TransitionMatrixGeneration(original_methyl,terminal_methyl)

ChengchenZhao/MethylTransition documentation built on Nov. 30, 2020, 11:09 a.m.