Nothing
# TODO: Add comment
#
# Author: ahrnee-adm
###############################################################################
### INIT
if(!grepl("SafeQuant\\.Rcheck",getwd())){
setwd(dirname(sys.frame(1)$ofile))
}
source("initTestSession.R")
### INIT END
### test functions
testGetImpuritiesMatrix <- function(){
cat(" --- testGetImpuritiesMatrix --- \n")
# 6-plex
# old stopifnot(0.094 == getImpuritiesMatrix(6)[1,2])
stopifnot(all.equal(0.004 , round(getImpuritiesMatrix(6)[1,2],3)))
# 10-plex
stopifnot(all.equal(0.004 , round(getImpuritiesMatrix(10)[1,2],3)))
cat(" --- testGetImpuritiesMatrix: PASS ALL TEST --- \n")
#getImpuritiesMatrix(test=T)
# getImpuritiesMatrix(test=T)
# [,1] [,2] [,3] [,4] [,5] [,6]
# [1,] 0.939 0.061 0.000 0.000 0.000 0.000
# [2,] 0.005 0.928 0.067 0.000 0.000 0.000
# [3,] 0.000 0.011 0.947 0.042 0.000 0.000
# [4,] 0.000 0.000 0.017 0.942 0.041 0.000
# [5,] 0.000 0.000 0.000 0.016 0.963 0.021
# [6,] 0.000 0.000 0.000 0.002 0.032 0.938
# > cat("Synch1432219972384675000\n");
}
testPurityCorrectTMT <- function(){
cat(" --- testPurityCorrectTMT --- \n")
# 6-plex
# old stopifnot( round(9.998839,4) == round(purityCorrectTMT(tmtTestData6Plex,impurityMatrix=getImpuritiesMatrix(6))[1,1],4))
stopifnot( all.equal(9.4965 , round(purityCorrectTMT(tmtTestData6Plex,impurityMatrix=getImpuritiesMatrix(6))[2,1],4)))
# 10-plex
stopifnot(all.equal(10.4493 , round(purityCorrectTMT(tmtTestData10Plex,impurityMatrix=getImpuritiesMatrix(10))[1,1],4)))
cat(" --- testPurityCorrectTMT: PASS ALL TEST --- \n")
}
testCreateExpDesign <- function(){
cat(" --- testCreateExpDesign --- \n")
stopifnot(sum(createExpDesign("1,2,3:4,5,6",6)$isControl == c(T,T,T,F,F,F)) == 6 )
stopifnot(sum(createExpDesign("10,2:3:4,5:6,7,8:9,1",10)$isControl == c(T,T,F,F,F,F,F,F,F,F)) == 10 )
stopifnot(sum(createExpDesign("10,2:3:4,5:6,7,8:9,1",10)$condition[1:2] == c("Ctrl","Ctrl")) == 2 )
stopifnot(length(unique(createExpDesign("10,2:3:4,5:6,7,8:9,1",10)$condition)) == 5 )
#createExpDesign("1,4,10:2,5,8:3,6,9",10)
cat(" --- testCreateExpDesign: PASS ALL TEST --- \n")
}
testGetCalibMixPairedEset <- function(){
cat("--- testGetCalibMixPairedEset: --- \n")
esetCalibMixPair <- .getCalibMixPairedEset(esetCalibMix)
stopifnot(ncol(esetCalibMixPair) == 2 )
stopifnot(nrow(esetCalibMixPair) == nrow(esetCalibMix)*5 )
cat("--- testGetCalibMixPairedEset: PASS ALL TEST --- \n")
}
### compare our impurity correction to MSnbase
#comparePurityCorrectionToMsnbase <- function(){
#
# cat(" --- comparePurityCorrectionToMsnbase --- \n")
#
# library(MSnbase)
#
# impurities <- matrix(c(0.929, 0.059, 0.002, 0.000,
# 0.020, 0.923, 0.056, 0.001,
# 0.000, 0.030, 0.924, 0.045,
# 0.000, 0.001, 0.040, 0.923),
# nrow = 4)
#
# qnt <- quantify(itraqdata[1:3,],reporters = iTRAQ4)
#
# exprs(qnt)[1,] <- rep(1,4)
# exprs(qnt)[2,] <- 1:4
#
# exprs(qnt)[3,] <- rnorm(4,10)
#
# qnt.crct <- purityCorrect(qnt, impurities)
#
# testA <- solve(impurities,rep(1,4))
# ### our correction method
# #testA <- as.vector(t(solve(impurities) %*% rep(1,4)))
# #testB <- as.vector(t(solve(impurities) %*% 1:4))
# testB <- solve(impurities,1:4)
# #testC <- as.vector(t(solve(impurities) %*% exprs(qnt)[3,]))
# testC <- solve(impurities,exprs(qnt)[3,])
#
# stopifnot( sum(round(testA,3) == round(exprs(qnt.crct)[1,],3)) == 4 )
# stopifnot( sum(round(testB,3) == round(exprs(qnt.crct)[2,],3)) == 4 )
# stopifnot( sum(round(testC,3) == round(exprs(qnt.crct)[3,],3)) == 4 )
#
# cat(" --- comparePurityCorrectionToMsnbase: PASS ALL TEST --- \n")
#
#
#}
testGetCalibMixEset <- function(){
cat("--- testGetCalibMixEset: --- \n")
esetCalibMix <- .getCalibMixEset(esetCalibMix)
stopifnot(nrow(esetCalibMix) == 437)
cat("--- testGetCalibMixEset: PASS ALL TEST --- \n")
}
testGetCalibMixPairedEset <- function(){
cat("--- testGetCalibMixPairedEset: --- \n")
esetCalibMixPair <- .getCalibMixPairedEset(.getCalibMixEset(esetCalibMix))
stopifnot(nrow(esetCalibMixPair) == 2185)
stopifnot(ncol(esetCalibMixPair) == 2)
cat("--- testGetCalibMixPairedEset: PASS ALL TEST --- \n")
}
#testGetRatioCorrectionFactorModel <- function(){
#
# cat("--- testGetRatioCorrectionFactorModel: --- \n")
# fit <- getRatioCorrectionFactorModel(rollUp(esetCalibMixPair))
# #stopifnot(round(coef(fit)[2],1) == 1.4)
# cat("--- testGetRatioCorrectionFactorModel: PASS ALL TEST --- \n")
#
#}
testIntensityAdjustment <- function(){
cat("--- testIntensityAdjustment: --- \n")
if(F){
load("/Users/ahrnee-adm/dev/R/workspace/SafeQuantTestData/rData/tmtRatioAdjTest.rData")
intAdjObj <- .intensityAdjustment(eset, esetCalibMix)
ratio <- getRatios(rollUp(sqNormalize(eset)))
ratioAdj <- getRatios(rollUp(sqNormalize(intAdjObj$esetAdj)))
lim <-c(-5,5)
plot(ratio[,3], ratioAdj[,3], ylim=lim, xlim=lim )
abline(coef=c(0,1),lty=2)
cor(as.vector(unlist(ratio[,1])), as.vector(unlist(ratioAdj[,1])))^2
lm( ratioAdj[,1] ~ ratio[,1])
esetCalMixAdjPaired <- .getCalibMixPairedEset(intAdjObj$esetCalMixAdj)
lim <-c(-4,4)
.plotTMTRatioVsRefRatio(rollUp(esetCalibMixPair, featureDataColumnName="proteinName"), ylim=lim, xlim=lim)
.plotTMTRatioVsRefRatio(rollUp(esetCalMixAdjPaired, featureDataColumnName="proteinName"), ylim=lim, xlim=lim)
}
expDesign <- data.frame(condition=paste("Condition",c(1,2,3,1,2,3,1,2,3,1),sep=""),isControl=c(T,F,F,T,F,F,T,F,F,T) )
esetTMT10Plex <- parseScaffoldRawFile(scaffoldTmt10PlexRawTestFile,expDesign = expDesign)
intAdjObj2 <- .intensityAdjustment(esetTMT10Plex, esetCalibMix)
stopifnot(round(intAdjObj2$globalNoiseFraction,3) == 0.193)
#barplot(apply(exprs(esetTMT10Plex),2,sum,na.rm=T))
cat("--- testIntensityAdjustment: PASS ALL TEST --- \n")
}
### test functions end
# INIT
### INIT END
### TESTS
if(F){
testGetImpuritiesMatrix()
testPurityCorrectTMT()
testCreateExpDesign()
testGetCalibMixEset()
testGetCalibMixPairedEset()
#testGetRatioCorrectionFactorModel()
testIntensityAdjustment()
}
#comparePurityCorrectionToMsnbase()
### TESTS END
#CALIBMIXRATIOS
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