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# Unit Tests for the nlcv package
#
# Tobias Verbeke
###############################################################################
### test on ALL data
test.nlcv <- function(){
require("ALL") # example data
data(ALL)
# create B-Cell subset for ALL and turn into a two-class problem
BCellSubset <- intersect(grep("^B", as.character(ALL$BT)),
which(ALL$mol %in% c("BCR/ABL","NEG")))
beset <- ALL[, BCellSubset]
beset$mol.biol <- beset$mol.biol[,drop=TRUE]
t.test_test_b <- nlcv(eset = beset, classVar = "mol.biol",
fsMethod = "t.test")
t.test_test_u <- nlcv(eset = beset, classVar = "mol.biol",
fsMethod = "t.test", classdist = "unbalanced")
limma_test_b <- nlcv(eset = beset, classVar = "mol.biol",
fsMethod = "limma")
limma_test_u <- nlcv(eset = beset, classVar = "mol.biol",
fsMethod = "limma", classdist = "unbalanced")
randomForest_test_b <- nlcv(eset = beset, classVar = "mol.biol",
fsMethod = "randomForest")
randomForest_test_u <- nlcv(eset = beset, classVar = "mol.biol",
fsMethod = "randomForest", classdist = "unbalanced")
return(randomForest_test_u)
}
test.topTable <- function(){
require(nlcv)
require(randomForest)
require("ALL") # example data
data(ALL)
# create B-Cell subset for ALL and turn into a two-class problem
BCellSubset <- intersect(grep("^B", as.character(ALL$BT)),
which(ALL$mol %in% c("BCR/ABL","NEG")))
beset <- ALL[, BCellSubset]
beset$mol.biol <- beset$mol.biol[,drop=TRUE]
nlcvObj <- nlcv(eset = beset, classVar = "mol.biol",
fsMethod = "randomForest", classdist = "unbalanced")
# checkException(topTable(nlcvObj)) # no n by default
topTable(nlcvObj, n = 15)
}
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