tests/test02.1-just.R

In ClassDiscovery: Classes and Methods for "Class Discovery" with Microarrays or Proteomics

library(ClassDiscovery)
suppressWarnings( RNGversion("3.5.3") )
set.seed(547422)
# simulate data from three different groups
d1 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
d2 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
d3 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
dd <- cbind(d1, d2, d3)

cutKmeans(dd, k=3)
cutKmeans(dd, k=4)

cutHclust(dd, k=3)
cutHclust(dd, k=4)

cutPam(dd, k=3)
cutPam(dd, k=4)

cutRepeatedKmeans(dd, k=3, nTimes=10)
crk <- cutRepeatedKmeans(dd, k=4, nTimes=10)
sort(as.vector(table(crk))) # sme numbers, different labels on some machines

# cleanup
rm(d1, d2, d3, dd)