inst/unitTests/test_cliquePairedTest.R

In clipper: Gene Set Analysis Exploiting Pathway Topology

library(gRbase)
library(MASS)

graph <- dag(c("me","ve"),c("me","al"),c("ve","al"),c("al","an"),c("al","st"),c("an","st"))

set.seed(1234)

sigma <- matrix(0,20,20)
diag(sigma)<-1

exp1 <-  mvrnorm(5, rep(5,20), sigma)
row.names(exp1)<-nodes(graph)

exp2 <- mvrnorm(5, rep(5,20), sigma)
row.names(exp2)<-nodes(graph)

colnames(exp1)<-LETTERS[1:20]
colnames(exp2)<-letters[1:20]
classes<-c(rep(2,20), rep(1,20))

exp <- cbind(exp1, exp2)


test_cliqueMeanTest <- function(){
  set.seed(1234)
  t <- cliquePairedTest(exp, classes, graph, 100)
  checkTrue(all(t$alpha > 0.01))
  checkEqualsNumeric(length(t),2)
  checkEqualsNumeric(length(t$cliques),2)
  checkException(cliquePairedTest(exp, classes[-1], graph, 100))
  row.names(exp) <- letters[1:5]
  checkException(cliquePairedTest(exp, classes, graph, 100))
}