Nothing
### INIT
if(!grepl("SafeQuant\\.Rcheck",getwd())){
setwd(dirname(sys.frame(1)$ofile))
}
source("initTestSession.R")
### INIT END
### TEST FUNCTIONS
testExport <-function(){
cat("--- testExport: --- \n")
sqa <- safeQuantAnalysis(eset)
export(sqa,file="~/tmp/tmp.csv")
cat("--- testExport: PASS ALL TEST --- \n")
}
testSafequantAnalysis <- function(){
cat("--- testSafequantAnalysis: --- \n")
sqa <- safeQuantAnalysis(eset)
stopifnot(sum(c("eset", "cv", "ratio", "pValue","qValue","baselineIntensity") %in% names(sqa)) == 6)
stopifnot(nrow(sqa$pValue) == nrow(sqa$eset) )
### filter our first 10 peptides
esetFiltered <- eset
fData(esetFiltered)$isFiltered[1:10] <- rep(T,10)
sqaFiltered <- safeQuantAnalysis(esetFiltered)
stopifnot(sum(is.na(sqaFiltered$pValue[,1])) == 10 )
stopifnot(sum(!is.na(sqaFiltered$pValue[,1])) == (nrow(sqaFiltered$pValue)-10))
# NA replace
esetNaRep <- eset
exprs(esetNaRep)[1,1] <- NA
stopifnot(!is.na(exprs(safeQuantAnalysis(esetNaRep, method=c("naRep"))$eset)[1,1]))
stopifnot(is.na(exprs(safeQuantAnalysis(esetNaRep, method=c(""))$eset)[1,1]))
esetTmp <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
sqaGlobal <- safeQuantAnalysis(esetTmp, method="global")
sqaRt <- safeQuantAnalysis(esetTmp, method="rt")
stopifnot(sum(sqaRt$pValue < 0.01) < sum(sqaGlobal$pValue < 0.01))
# TMT ratio correction
# fit <- getRatioCorrectionFactorModel(rollUp(esetCalibMixPair))
# sqaTMTCorrected <- safeQuantAnalysis(esetCalibMix, ratioCorrectionModel=fit, method=c(""))
# rTmp <- getRatios(esetCalibMix)
# stopifnot(all(abs(sqaTMTCorrected$ratio) >= abs(rTmp)))
# stopifnot(round(sqaTMTCorrected$ratio[1,2],2) == round( rTmp[1,2]*coef(fit)[2] ,2))
# stopifnot(round(sqaTMTCorrected$ratio[400,2],2) == round( rTmp[400,2]*coef(fit)[2] ,2))
# stopifnot(all(safeQuantAnalysis(esetCalibMix, method=c(""))$pValue == sqaTMTCorrected$pValue))
#
# ratio filter multiple testing
sqaRatioMT <- safeQuantAnalysis(eset,fcThrs =2^quantile(getRatios(eset)[,1])[2])
stopifnot(sum(is.na(sqaRatioMT$qValue[,1])) > 400)
cat("--- testSafequantAnalysis: PASS ALL TEST --- \n")
}
### TEST FUNCTIONS END
### TESTS
#testExport()
testSafequantAnalysis()
#sqa <- safeQuantAnalysis(eset)
#print(sqa)
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