# TODO: Add comment
#
# Author: ahrnee-adm
###############################################################################
### INIT
if(!grepl("SafeQuant\\.Rcheck",getwd())){
setwd(dirname(sys.frame(1)$ofile))
}
source("initTestSession.R")
### INIT END
### TEST FUNCTIONS
################## TMT ##################
testGetSkipLineNb <- function(){
cat(" --- testGetSkipLineNb --- \n")
stopifnot(40 == .getSkipLineNb(scaffoldTmt6PlexRawTestFile))
stopifnot(40 == .getSkipLineNb(scaffoldTmt10PlexRawTestFile))
cat(" --- testGetSkipLineNb: PASS ALL TEST --- \n")
}
testGetNbPlex <- function(){
cat(" --- testGetNbPlex --- \n")
stopifnot(10 ==.getNbPlex(scaffoldTmt10PlexRawTestFile))
stopifnot(6 ==.getNbPlex(scaffoldTmt6PlexRawTestFile))
cat(" --- testGetNbPlex: PASS ALL TEST --- \n")
}
################## LFQ ##################
testGetProgenesisCsvExpressionColIndices <- function(){
cat(" --- testGetProgenesisCsvProteinIntColIndices --- \n")
stopifnot(sum(14:17 %in% .getProgenesisCsvExpressionColIndices(progenesisProteinCsvFile1) ) == 4 )
stopifnot(sum(31:48 %in% .getProgenesisCsvExpressionColIndices(progenesisFeatureCsvFile1) ) == 18 )
stopifnot(.getProgenesisCsvExpressionColIndices(progenesisPeptideMeasurementCsvFile1) == 18 )
stopifnot(.getProgenesisCsvExpressionColIndices(progenesisPeptideMeasurementFractionatedCsvFile1)[1] == 21)
cat(" --- testGetProgenesisCsvProteinIntColIndices: PASS ALL TEST --- \n")
}
testGetExpDesignProgenesisCsv <- function(){
cat(" --- testGetExpDesignProgenesisCsv --- \n")
stopifnot(4 == nrow( getExpDesignProgenesisCsv(progenesisProteinCsvFile1) ))
stopifnot(18 == nrow(getExpDesignProgenesisCsv(progenesisFeatureCsvFile1) ))
cat(" --- testGetExpDesignProgenesisCsv: PASS ALL TEST --- \n")
}
testParseProgenesisProteinCsv <- function(){
cat(" --- testParseProgenesisProteinCsv --- \n")
eset <- parseProgenesisProteinCsv(file=progenesisProteinCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisProteinCsvFile1))
stopifnot(983 == nrow(eset))
stopifnot(8 == ncol(fData(eset)))
stopifnot(4 == nrow(pData(eset)))
expDesign <- getExpDesignProgenesisCsv(progenesisProteinCsvFile1)[c(3,2),]
eset2 <- parseProgenesisProteinCsv(file=progenesisProteinCsvFile1,expDesign=expDesign)
stopifnot(colnames(eset2) == row.names(pData(eset))[c(3,2)] )
### change expDesign
cat(" --- testParseProgenesisProteinCsv: PASS ALL TEST --- \n")
}
testParseProgenesisFeatureCsv <- function(){
cat(" --- testParseProgenesisFeatureCsv --- \n")
eset <- parseProgenesisFeatureCsv(file=progenesisFeatureCsvFile1,expDesign=getExpDesignProgenesisCsv(progenesisFeatureCsvFile1))
stopifnot(97 == nrow(eset))
#names(fData(eset))
stopifnot(15 == ncol(fData(eset)))
stopifnot(18 == nrow(pData(eset)))
# expDesign <- getExpDesignProgenesisCsv(progenesisFeatureCsvFile1)[c(3,4:8),]
# eset2 <- parseProgenesisPeptideCsv(file=progenesisFeatureCsvFile1,expDesign=expDesign)
#
# pData(eset2)
# pData(eset)
cat(" --- testParseProgenesisFeatureCsv: PASS ALL TEST --- \n")
}
testParseScaffoldRawFile <- function(){
cat(" --- testParseScaffoldRawFile --- \n")
# 6 plex
expDesignTMTSixPlex <- data.frame(condition=sort(rep(c(1,2),3)),isControl=sort(rep(c(T,F),3),decreasing=T) )
eset <- parseScaffoldRawFile(scaffoldTmt6PlexRawTestFile,expDesign=expDesignTMTSixPlex)
stopifnot(329 == nrow(eset))
stopifnot("sp|P38711|RS27B_YEAST,sp|P35997|RS27_YEAST" == fData(eset)$proteinName[1])
stopifnot("sp|P38711|RS27B_YEAST" == fData(parseScaffoldRawFile(scaffoldTmt6PlexRawTestFile,expDesign=expDesignTMTSixPlex,keepFirstAcOnly=T))$proteinName[1])
expDesignTMTSixPlex <- data.frame(condition=sort(rep(c(1,2),3)),isControl=sort(rep(c(T,F),3),decreasing=T) )
rownames(expDesignTMTSixPlex) <- rev(1:6)
eset2 <- parseScaffoldRawFile(scaffoldTmt6PlexRawTestFile,expDesign=expDesignTMTSixPlex[1:5,])
stopifnot(all.equal(exprs(eset)[1,6], exprs(eset2)[1,1]))
# 10 plex
expDesignTMTTenPlex <- data.frame(condition=sort(rep(c(1:5),2)),isControl=c(T,T,rep(F,8)) )
eset3 <- parseScaffoldRawFile(scaffoldTmt10PlexRawTestFile,expDesign=expDesignTMTTenPlex, keepFirstAcOnly=T)
stopifnot(958 == nrow(eset3))
cat(" --- testParseScaffoldRawFile: PASS ALL TEST --- \n")
}
testGetFileType <- function(){
cat(" --- testGetFileType --- \n")
stopifnot(.getFileType(scaffoldTmt6PlexRawTestFile) == "ScaffoldTMT")
stopifnot(.getFileType(scaffoldTmt10PlexRawTestFile) == "ScaffoldTMT")
stopifnot(.getFileType(progenesisFeatureCsvFile1) == "ProgenesisFeature")
stopifnot(.getFileType(progenesisProteinCsvFile1) == "ProgenesisProtein")
stopifnot(.getFileType(progenesisPeptideMeasurementCsvFile1) == "ProgenesisPeptide")
stopifnot(.getFileType(maxQuantProteinFileTxt) == "MaxQuantProteinGroup")
cat(" --- testGetFileType: PASS ALL TEST --- \n")
}
testParseProgenesisPeptideMeasurementCsv <- function(){
cat(" --- testParseProgenesisPeptideMeasurementCsv --- \n")
eset <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1))
stopifnot(ncol(exprs(eset)) == 1)
stopifnot(nrow(eset) == 92)
stopifnot(sum(grepl(";",fData(eset)$proteinName)) == 2)
stopifnot("sp|Q9Y6H1|CHCH2_HUMAN;sp|Q5T1J5|CHCH9_HUMAN" %in% fData(eset)$proteinName)
stopifnot(all.equal(which(fData(eset)$nbProteinConflicts == 1), c(33,66)))
esetUnique <- parseProgenesisPeptideMeasurementCsv(progenesisPeptideMeasurementCsvFile1,expDesign= getExpDesignProgenesisCsv(progenesisPeptideMeasurementCsvFile1), exclusivePeptides = T)
stopifnot(sum(fData(esetUnique)$nbProteinConflicts) == 0)
cat(" --- testParseProgenesisPeptideMeasurementCsv: PASS ALL TEST --- \n")
}
testParseMaxQuantProteinGroupTxt <- function(){
cat(" --- testParseMaxQuantProteinGroupTxt: --- \n")
expDesign <- data.frame(row.names=1:20,isControl=c(rep(T,5),rep(F,15)),condition=sort(rep(paste("condition",1:4,sep="_"),5)))
eset <- parseMaxQuantProteinGroupTxt(maxQuantProteinFileTxt,expDesign=expDesign, method="auc")
stopifnot(ncol(fData(eset)) == 9)
stopifnot(ncol(eset) == 20)
stopifnot( nrow(parseMaxQuantProteinGroupTxt(maxQuantProteinFileTxt,expDesign=expDesign, method="spc")) == 996 )
cat(" --- testParseMaxQuantProteinGroupTxt: PASS ALL TEST --- \n")
}
testParseScaffoldPTMReport <- function(){
cat(" --- testParseScaffoldPTMReport: --- \n")
df <- parseScaffoldPTMReport(scaffoldPtmReportFile1)
stopifnot(nrow(df) == 883 )
cat(" --- testParseScaffoldPTMReport: PASS ALL TEST --- \n")
}
testAddScaffoldPTMFAnnotations <- function(){
expDesignTMTTenPlex <- data.frame(condition=sort(rep(c(1:5),2)),isControl=c(T,T,rep(F,8)) )
eset <- parseScaffoldRawFile(scaffoldPtmTMTRawDataFile1,expDesign = expDesignTMTTenPlex)
cat(" --- testAddScaffoldPTMFAnnotations: --- \n")
eset <- addScaffoldPTMFAnnotations(eset,scaffoldPtmReportFile1)
stopifnot(all( c("ptmPeptide","ptm","ptmLocProb","idScore","ptmLocMascotConfidence","pMassError") %in% names(fData(eset))))
cat(" --- testAddScaffoldPTMFAnnotations: PASS ALL TEST --- \n")
}
### TEST FUNCTIONS END
#testParseProgenesisPeptideMeasurementCsv()
### TESTS
if(T){
testGetFileType()
# progenesis
testGetProgenesisCsvExpressionColIndices()
testGetExpDesignProgenesisCsv()
testParseProgenesisProteinCsv()
testParseProgenesisFeatureCsv()
testParseProgenesisPeptideMeasurementCsv()
# scaffold
testGetSkipLineNb()
testParseScaffoldRawFile()
testGetNbPlex()
testParseScaffoldPTMReport()
testAddScaffoldPTMFAnnotations()
# max quant
testParseMaxQuantProteinGroupTxt()
}
### TESTS END
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