Experiments

Code for experiments

Simulation

Real data

Example

data(ExampleData)
geno <- ExampleData$geno
K <- ExampleData$K
data <- ExampleData$data
res=image(geno,data,K)

An example of the outputs IMAGE produces:

data(example_results)

A toy example for testing purposes only:

geno <- list()
geno$hap1 = matrix(sample(c(0,1),25, replace = TRUE, prob = c(0.6,0.4)),
                    nrow = 5, ncol = 5)
geno$hap2 = matrix(sample(c(0,1),25, replace = TRUE, prob = c(0.6,0.4)),
                    nrow = 5, ncol = 5)

data <- list()
data$r = matrix(sample(0:50,25, replace = TRUE), nrow = 5, ncol = 5)
data$y = matrix(sample(0:50,25, replace = TRUE), nrow = 5, ncol = 5)
data$r1 = matrix(sample(0:50,25, replace = TRUE), nrow = 5, ncol = 5)
data$r2 = matrix(sample(0:50,25, replace = TRUE), nrow = 5, ncol = 5)
data$y1 = matrix(sample(0:50,25, replace = TRUE), nrow = 5, ncol = 5)
data$y2 = matrix(sample(0:50,25, replace = TRUE), nrow = 5, ncol = 5)

K = matrix(runif(25,-0.1,0.1), nrow = 5, ncol = 5)

res=image(geno,data,K)

To normalize the pvalues:

p<-res[,5]
chisq <- qchisq(1-p,1)
lambda=median(chisq)/qchisq(0.5,1)
chisq=chisq/lambda
pvalue=pchisq( chisq, 1, lower.tail = F)