inst/examples/coseq-package.R

In coseq: Co-Expression Analysis of Sequencing Data

## Simulate toy data, n = 300 observations
set.seed(12345)
countmat <- matrix(runif(300*4, min=0, max=500), nrow=300, ncol=4)
countmat <- countmat[which(rowSums(countmat) > 0),]
conds <- rep(c("A","B","C","D"), each=2)

## Run the Normal mixture model for K = 2,3,4
run_arcsin <- coseq(y=countmat, K=2:4, iter=5, transformation="arcsin")

## Plot and summarize results
plot(run_arcsin)
summary(run_arcsin)

## Compare ARI values for all models (no plot generated here)
ARI <- compareARI(run_arcsin, plot=FALSE)

## Compare ICL values for models with arcsin and logit transformations
run_logit <- coseq(y=countmat, K=2:4, iter=5, transformation="logit")
compareICL(list(run_arcsin, run_logit))