SimulateData: Simulate data under certain graphs

In audreyqyfu/mrpc2: PC Algorithm with the Principle of Mendelian Randomization

Simulate data under certain graphs

Description

This function simulates data using linear models for several graphs: the five basic topologies and three topologies that are common in biology, namely the multi-parent graph, the star graph and the layered graph. See details in Badsha and Fu (2019) and Badsha et al. (2021).

Usage

SimulateData(N, p, model, b0.1, b1.1, b1.2, b1.3, sd.1)

Arguments

N	The number of observations.
p	Population frequency of the reference allele. Real number between 0 to 1, which is the number of a particular allele is present.
model	The model for which data will be simulated. For example, if you want to generate data for model 0 you would type 'model0' into the function.
b0.1	Intercept of b0.1 + b1.1*P1 + b1.2*P2 + b1.3*P3, where P1, P2, and P3 are the parents of the corresponding node.
b1.1	Slope of P1 for b0.1 + b1.1*P1 + b1.2*P2 + b1.3*P3, where P1, P2, and P3 are the parents of the corresponding node.
b1.2	Slope of P2 for b0.1 + b1.1*P1 + b1.2*P2 + b1.3*P3, where P1, P2, and P3 are the parents of the corresponding node.
b1.3	Slope of P3 for b0.1 + b1.1*P1 + b1.2*P2 + b1.3*P3, where P1, P2, and P3 are the parents of the corresponding node.
sd.1	Standard deviation for corresponding data generated nodes.

Details

The first column of the input matrix is a genetic variant and the remaining columns are gene expression nodes.

Value

Matrix

Author(s)

Md Bahadur Badsha ([e-mail])

References

1. Badsha MB and Fu AQ (2019). Learning causal biological networks with the principle of Mendelian randomization. Frontiers in Genetics, 10:460.

2. Badsha MB, Martin EA and Fu AQ (2021). MRPC: An R package for inference of causal graphs. Frontiers in Genetics, 10:651812.

See Also

MRPC; SimulateDataNP, which simulates data for a node with no parent; SimulateData1P for a node with one parent; SimulateData2P for a node with two parents.

Examples

# When there is one genetic variant, the 1st column of
# the simulated data matrix will be the variant and the remaining
# columns are the gene expression nodes.


## Model 0
simu_data_M0 <- SimulateData(N = 10^3, 
                             p = 0.45,
                             'model0', 
                             b0.1 = 0,
                             b1.1 = 1, 
                             b1.2 = 1,
                             b1.3 = 1, 
                             sd.1 = 1)
                             
## Model 1
simu_data_M1 <- SimulateData(N = 10^3, 
                             p = 0.45,
                             'model1', 
                             b0.1 = 0,
                             b1.1 = 1, 
                             b1.2 = 1,
                             b1.3 = 1, 
                             sd.1 = 1)
                             
## Model 2
simu_data_M2 <- SimulateData(N = 10^3, 
                             p = 0.45,
                             'model2', 
                             b0.1 = 0,
                             b1.1 = 1, 
                             b1.2 = 1,
                             b1.3 = 1, 
                             sd.1 = 1)
                             
## Model 3
simu_data_M3 <- SimulateData(N = 10^3, 
                             p = 0.45,
                             'model3', 
                             b0.1 = 0,
                             b1.1 = 1, 
                             b1.2 = 1,
                             b1.3 = 1, 
                             sd.1 = 1)
                             
## Model 4
simu_data_M4 <- SimulateData(N = 10^3, 
                             p = 0.45,
                             'model4', 
                             b0.1 = 0,
                             b1.1 = 1, 
                             b1.2 = 1,
                             b1.3 = 1, 
                             sd.1 = 1)
                             
## Multiple Parent Model
simu_data_multiparent <- SimulateData(N = 10^3, 
                                      p = 0.45,
                                      'multiparent', 
                                      b0.1 = 0,
                                      b1.1 = 1, 
                                      b1.2 = 1,
                                      b1.3 = 1, 
                                      sd.1 = 1)

## Star Model
simu_data_starshaped <- SimulateData(N = 10^3, 
                                     p = 0.45,
                                     'starshaped', 
                                     b0.1 = 0,
                                     b1.1 = 1, 
                                     b1.2 = 1,
                                     b1.3 = 1, 
                                     sd.1 = 1)

## Layered Model
simu_data_layered <- SimulateData(N = 10^3, 
                                  p = 0.45,
                                  'layered', 
                                  b0.1 = 0,
                                  b1.1 = 1, 
                                  b1.2 = 1,
                                  b1.3 = 1, 
                                  sd.1 = 1)

audreyqyfu/mrpc2 documentation built on April 17, 2022, 7:36 a.m.