Nothing
############################################################################
#' test_utils.R
#'
#' Tests for the imputation, CNV estimation and age prediction methods in RnBeads
############################################################################
#test_cnv <- function(){
# require(RnBeads.hg19)
# dir.report <- file.path(tempdir(),"report43/")
# unlink(dir.report,recursive = TRUE)
# report <- createReport(file.path(dir.report,'index.html'),'MyReport',init.configuration=TRUE)
# data(small.example.object)
# report <- rnb.step.cnv(rnb.set.example,report)
# passed <- inherits(report,"Report")
# unlink(dir.report,recursive = TRUE)
# checkTrue(passed)
#}
test_imputation <- function(){
require(RnBeads.hg19)
data(small.example.object)
methData <- meth(rnb.set.example)
methData <- apply(methData,2,function(x){
x[sample(1:length(x),42)] <- NA
x
})
rnb.set.example@meth.sites <- methData
rnb.set.knn <- rnb.execute.imputation(rnb.set.example,method = "knn")
rnb.set.samples <- rnb.execute.imputation(rnb.set.example,method = "mean.samples")
rnb.set.cpgs <- rnb.execute.imputation(rnb.set.example,method = "mean.cpgs")
rnb.set.random <- rnb.execute.imputation(rnb.set.example,method = "random")
passed <- !(any(is.na(meth(rnb.set.knn)))) && !(any(is.na(meth(rnb.set.samples)))) && !(any(is.na(meth(rnb.set.cpgs)))) && !(any(is.na(meth(rnb.set.random))))
checkTrue(passed)
}
test_age.prediction <- function(){
require(RnBeads.hg19)
data(small.example.object)
rnb.set.example <- rnb.execute.age.prediction(rnb.set.example)
ph <- pheno(rnb.set.example)
passed <- is.element("predicted_ages",colnames(ph)) && all(is.numeric(ph$predicted_ages))
checkTrue(passed)
}
test_utils <- function(){
logger.start("Testing imputation")
test_imputation()
logger.completed()
logger.start("Testing age prediction")
test_age.prediction()
logger.completed()
# logger.start("Testing CNV computation")
# test_cnv()
# logger.completed()
}
test_utils()
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.