Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2025-04-02 19:31 -0400 (Wed, 02 Apr 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 93/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
aroma.light 3.36.0 (landing page) Henrik Bengtsson
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the aroma.light package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/aroma.light.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: aroma.light |
Version: 3.36.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:aroma.light.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings aroma.light_3.36.0.tar.gz |
StartedAt: 2025-03-31 23:23:14 -0400 (Mon, 31 Mar 2025) |
EndedAt: 2025-03-31 23:25:54 -0400 (Mon, 31 Mar 2025) |
EllapsedTime: 160.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: aroma.light.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:aroma.light.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings aroma.light_3.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/aroma.light.Rcheck’ * using R version 4.4.3 (2025-02-28) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘aroma.light/DESCRIPTION’ ... OK * this is package ‘aroma.light’ version ‘3.36.0’ * package encoding: latin1 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: inst/rsp/.rspPlugins These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘aroma.light’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed normalizeCurveFit 12.156 0.155 13.316 normalizeAffine 11.917 0.163 13.247 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘backtransformAffine.matrix.R’ Running ‘backtransformPrincipalCurve.matrix.R’ Running ‘callNaiveGenotypes.R’ Running ‘distanceBetweenLines.R’ Running ‘findPeaksAndValleys.R’ Running ‘fitPrincipalCurve.matrix.R’ Running ‘fitXYCurve.matrix.R’ Running ‘iwpca.matrix.R’ Running ‘likelihood.smooth.spline.R’ Running ‘medianPolish.matrix.R’ Running ‘normalizeAffine.matrix.R’ Running ‘normalizeAverage.list.R’ Running ‘normalizeAverage.matrix.R’ Running ‘normalizeCurveFit.matrix.R’ Running ‘normalizeDifferencesToAverage.R’ Running ‘normalizeFragmentLength-ex1.R’ Running ‘normalizeFragmentLength-ex2.R’ Running ‘normalizeQuantileRank.list.R’ Running ‘normalizeQuantileRank.matrix.R’ Running ‘normalizeQuantileSpline.matrix.R’ Running ‘normalizeTumorBoost,flavors.R’ Running ‘normalizeTumorBoost.R’ Running ‘robustSmoothSpline.R’ Running ‘rowAverages.matrix.R’ Running ‘sampleCorrelations.matrix.R’ Running ‘sampleTuples.R’ Running ‘wpca.matrix.R’ Running ‘wpca2.matrix.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/aroma.light.Rcheck/00check.log’ for details.
aroma.light.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL aroma.light ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘aroma.light’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (aroma.light)
aroma.light.Rcheck/tests/backtransformAffine.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > X <- matrix(1:8, nrow=4, ncol=2) > X[2,2] <- NA_integer_ > > print(X) [,1] [,2] [1,] 1 5 [2,] 2 NA [3,] 3 7 [4,] 4 8 > > # Returns a 4x2 matrix > print(backtransformAffine(X, a=c(1,5))) [,1] [,2] [1,] 0 0 [2,] 1 NA [3,] 2 2 [4,] 3 3 > > # Returns a 4x2 matrix > print(backtransformAffine(X, b=c(1,1/2))) [,1] [,2] [1,] 1 10 [2,] 2 NA [3,] 3 14 [4,] 4 16 > > # Returns a 4x2 matrix > print(backtransformAffine(X, a=matrix(1:4,ncol=1))) [,1] [,2] [1,] 0 4 [2,] 0 NA [3,] 0 4 [4,] 0 4 > > # Returns a 4x2 matrix > print(backtransformAffine(X, a=matrix(1:3,ncol=1))) [,1] [,2] [1,] 0 4 [2,] 0 NA [3,] 0 4 [4,] 3 7 > > # Returns a 4x2 matrix > print(backtransformAffine(X, a=matrix(1:2,ncol=1), b=c(1,2))) [,1] [,2] [1,] 0 2 [2,] 0 NA [3,] 2 3 [4,] 2 3 > > # Returns a 4x1 matrix > print(backtransformAffine(X, b=c(1,1/2), project=TRUE)) [,1] [1,] 2.8 [2,] 1.6 [3,] 5.2 [4,] 6.4 > > # If the columns of X are identical, and a identity > # backtransformation is applied and projected, the > # same matrix is returned. > X <- matrix(1:4, nrow=4, ncol=3) > Y <- backtransformAffine(X, b=c(1,1,1), project=TRUE) > print(X) [,1] [,2] [,3] [1,] 1 1 1 [2,] 2 2 2 [3,] 3 3 3 [4,] 4 4 4 > print(Y) [,1] [1,] 1 [2,] 2 [3,] 3 [4,] 4 > stopifnot(sum(X[,1]-Y) <= .Machine$double.eps) > > > # If the columns of X are identical, and a identity > # backtransformation is applied and projected, the > # same matrix is returned. > X <- matrix(1:4, nrow=4, ncol=3) > X[,2] <- X[,2]*2; X[,3] <- X[,3]*3 > print(X) [,1] [,2] [,3] [1,] 1 2 3 [2,] 2 4 6 [3,] 3 6 9 [4,] 4 8 12 > Y <- backtransformAffine(X, b=c(1,2,3)) > print(Y) [,1] [,2] [,3] [1,] 1 1 1 [2,] 2 2 2 [3,] 3 3 3 [4,] 4 4 4 > Y <- backtransformAffine(X, b=c(1,2,3), project=TRUE) > print(Y) [,1] [1,] 1 [2,] 2 [3,] 3 [4,] 4 > stopifnot(sum(X[,1]-Y) <= .Machine$double.eps) > > proc.time() user system elapsed 0.512 0.143 0.643
aroma.light.Rcheck/tests/backtransformPrincipalCurve.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Consider the case where K=4 measurements have been done > # for the same underlying signals 'x'. The different measurements > # have different systematic variation > # > # y_k = f(x_k) + eps_k; k = 1,...,K. > # > # In this example, we assume non-linear measurement functions > # > # f(x) = a + b*x + x^c + eps(b*x) > # > # where 'a' is an offset, 'b' a scale factor, and 'c' an exponential. > # We also assume heteroscedastic zero-mean noise with standard > # deviation proportional to the rescaled underlying signal 'x'. > # > # Furthermore, we assume that measurements k=2 and k=3 undergo the > # same transformation, which may illustrate that the come from > # the same batch. However, when *fitting* the model below we > # will assume they are independent. > > # Transforms > a <- c(2, 15, 15, 3) > b <- c(2, 3, 3, 4) > c <- c(1, 2, 2, 1/2) > K <- length(a) > > # The true signal > N <- 1000 > x <- rexp(N) > > # The noise > bX <- outer(b,x) > E <- apply(bX, MARGIN=2, FUN=function(x) rnorm(K, mean=0, sd=0.1*x)) > > # The transformed signals with noise > Xc <- t(sapply(c, FUN=function(c) x^c)) > Y <- a + bX + Xc + E > Y <- t(Y) > > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Fit principal curve > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Fit principal curve through Y = (y_1, y_2, ..., y_K) > fit <- fitPrincipalCurve(Y) > > # Flip direction of 'lambda'? > rho <- cor(fit$lambda, Y[,1], use="complete.obs") > flip <- (rho < 0) > if (flip) { + fit$lambda <- max(fit$lambda, na.rm=TRUE)-fit$lambda + } > > L <- ncol(fit$s) > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Backtransform data according to model fit > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Backtransform toward the principal curve (the "common scale") > YN1 <- backtransformPrincipalCurve(Y, fit=fit) > stopifnot(ncol(YN1) == K) > > > # Backtransform toward the first dimension > YN2 <- backtransformPrincipalCurve(Y, fit=fit, targetDimension=1) > stopifnot(ncol(YN2) == K) > > > # Backtransform toward the last (fitted) dimension > YN3 <- backtransformPrincipalCurve(Y, fit=fit, targetDimension=L) > stopifnot(ncol(YN3) == K) > > > # Backtransform toward the third dimension (dimension by dimension) > # Note, this assumes that K == L. > YN4 <- Y > for (cc in 1:L) { + YN4[,cc] <- backtransformPrincipalCurve(Y, fit=fit, + targetDimension=1, dimensions=cc) + } > stopifnot(identical(YN4, YN2)) > > > # Backtransform a subset toward the first dimension > # Note, this assumes that K == L. > YN5 <- backtransformPrincipalCurve(Y, fit=fit, + targetDimension=1, dimensions=2:3) > stopifnot(identical(YN5, YN2[,2:3])) > stopifnot(ncol(YN5) == 2) > > > # Extract signals from measurement #2 and backtransform according > # its model fit. Signals are standardized to target dimension 1. > y6 <- Y[,2,drop=FALSE] > yN6 <- backtransformPrincipalCurve(y6, fit=fit, dimensions=2, + targetDimension=1) > stopifnot(identical(yN6, YN2[,2,drop=FALSE])) > stopifnot(ncol(yN6) == 1) > > > # Extract signals from measurement #2 and backtransform according > # the the model fit of measurement #3 (because we believe these > # two have undergone very similar transformations. > # Signals are standardized to target dimension 1. > y7 <- Y[,2,drop=FALSE] > yN7 <- backtransformPrincipalCurve(y7, fit=fit, dimensions=3, + targetDimension=1) > stopifnot(ncol(yN7) == 1) > > rho <- cor(yN7, yN6) > print(rho) [,1] [1,] 0.9999834 > stopifnot(rho > 0.999) > > proc.time() user system elapsed 1.488 0.201 1.746
aroma.light.Rcheck/tests/callNaiveGenotypes.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > layout(matrix(1:3, ncol=1)) > par(mar=c(2,4,4,1)+0.1) > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # A bimodal distribution > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > xAA <- rnorm(n=10000, mean=0, sd=0.1) > xBB <- rnorm(n=10000, mean=1, sd=0.1) > x <- c(xAA,xBB) > fit <- findPeaksAndValleys(x) > print(fit) type x density 1 peak -0.005370629 1.6656155900 2 valley 0.492846580 0.0004048371 3 peak 0.999728436 1.6891494528 > calls <- callNaiveGenotypes(x, cn=rep(1,length(x)), verbose=-20) Calling genotypes from allele B fractions (BAFs)... Fitting naive genotype model... Fitting naive genotype model from normal allele B fractions (BAFs)... Flavor: density Censoring BAFs... Before: Min. 1st Qu. Median Mean 3rd Qu. Max. -0.443399 -0.001602 0.469774 0.500033 1.001431 1.390101 [1] 20000 After: Min. 1st Qu. Median Mean 3rd Qu. Max. -Inf -0.001602 0.469774 1.001431 Inf [1] 16816 Censoring BAFs...done Copy number level #1 (C=1) of 1... Identified extreme points in density of BAF: type x density 1 peak 0.01098446 1.620230686 2 valley 0.49830030 0.004019183 3 peak 0.98218433 1.636719225 Local minimas ("valleys") in BAF: type x density 2 valley 0.4983003 0.004019183 Copy number level #1 (C=1) of 1...done Fitting naive genotype model from normal allele B fractions (BAFs)...done [[1]] [[1]]$flavor [1] "density" [[1]]$cn [1] 1 [[1]]$nbrOfGenotypeGroups [1] 2 [[1]]$tau [1] 0.4983003 [[1]]$n [1] 16816 [[1]]$fit type x density 1 peak 0.01098446 1.620230686 2 valley 0.49830030 0.004019183 3 peak 0.98218433 1.636719225 [[1]]$fitValleys type x density 2 valley 0.4983003 0.004019183 attr(,"class") [1] "NaiveGenotypeModelFit" "list" Fitting naive genotype model...done Copy number level #1 (C=1) of 1... Model fit: $flavor [1] "density" $cn [1] 1 $nbrOfGenotypeGroups [1] 2 $tau [1] 0.4983003 $n [1] 16816 $fit type x density 1 peak 0.01098446 1.620230686 2 valley 0.49830030 0.004019183 3 peak 0.98218433 1.636719225 $fitValleys type x density 2 valley 0.4983003 0.004019183 Genotype threshholds [1]: 0.498300295777735 TCN=1 => BAF in {0,1}. Call regions: A = (-Inf,0.498], B = (0.498,+Inf) Copy number level #1 (C=1) of 1...done Calling genotypes from allele B fractions (BAFs)...done > xc <- split(x, calls) > print(table(calls)) calls 0 1 10000 10000 > xx <- c(list(x),xc) > plotDensity(xx, adjust=1.5, lwd=2, col=seq_along(xx), main="(AA,BB)") > abline(v=fit$x) > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # A trimodal distribution with missing values > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > xAB <- rnorm(n=10000, mean=1/2, sd=0.1) > x <- c(xAA,xAB,xBB) > x[sample(length(x), size=0.05*length(x))] <- NA_real_ > x[sample(length(x), size=0.01*length(x))] <- -Inf > x[sample(length(x), size=0.01*length(x))] <- +Inf > fit <- findPeaksAndValleys(x) > print(fit) type x density 1 peak -0.007364773 1.1589050 2 valley 0.246519813 0.1881196 3 peak 0.496242357 1.1709918 4 valley 0.745964901 0.1878704 5 peak 0.999849488 1.1645934 > calls <- callNaiveGenotypes(x) > xc <- split(x, calls) > print(table(calls)) calls 0 0.5 1 9613 9328 9595 > xx <- c(list(x),xc) > plotDensity(xx, adjust=1.5, lwd=2, col=seq_along(xx), main="(AA,AB,BB)") > abline(v=fit$x) > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # A trimodal distribution with clear separation > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > xAA <- rnorm(n=10000, mean=0, sd=0.02) > xAB <- rnorm(n=10000, mean=1/2, sd=0.02) > xBB <- rnorm(n=10000, mean=1, sd=0.02) > x <- c(xAA,xAB,xBB) > fit <- findPeaksAndValleys(x) > print(fit) type x density 1 peak -0.00277501 2.603715e+00 2 valley 0.24862300 3.103390e-05 3 peak 0.49722770 2.610496e+00 4 valley 0.74583240 3.216145e-05 5 peak 0.99723042 2.609777e+00 > calls <- callNaiveGenotypes(x) > xc <- split(x, calls) > print(table(calls)) calls 0 0.5 1 10000 10000 10000 > xx <- c(list(x),xc) > plotDensity(xx, adjust=1.5, lwd=2, col=seq_along(xx), main="(AA',AB',BB')") > abline(v=fit$x) > > proc.time() user system elapsed 1.009 0.172 1.182
aroma.light.Rcheck/tests/distanceBetweenLines.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > for (zzz in 0) { + + # This example requires plot3d() in R.basic [http://www.braju.com/R/] + if (!require(pkgName <- "R.basic", character.only=TRUE)) break + + layout(matrix(1:4, nrow=2, ncol=2, byrow=TRUE)) + + ############################################################ + # Lines in two-dimensions + ############################################################ + x <- list(a=c(1,0), b=c(1,2)) + y <- list(a=c(0,2), b=c(1,1)) + fit <- distanceBetweenLines(ax=x$a, bx=x$b, ay=y$a, by=y$b) + + xlim <- ylim <- c(-1,8) + plot(NA, xlab="", ylab="", xlim=ylim, ylim=ylim) + + # Highlight the offset coordinates for both lines + points(t(x$a), pch="+", col="red") + text(t(x$a), label=expression(a[x]), adj=c(-1,0.5)) + points(t(y$a), pch="+", col="blue") + text(t(y$a), label=expression(a[y]), adj=c(-1,0.5)) + + v <- c(-1,1)*10 + xv <- list(x=x$a[1]+x$b[1]*v, y=x$a[2]+x$b[2]*v) + yv <- list(x=y$a[1]+y$b[1]*v, y=y$a[2]+y$b[2]*v) + + lines(xv, col="red") + lines(yv, col="blue") + + points(t(fit$xs), cex=2.0, col="red") + text(t(fit$xs), label=expression(x(s)), adj=c(+2,0.5)) + points(t(fit$yt), cex=1.5, col="blue") + text(t(fit$yt), label=expression(y(t)), adj=c(-1,0.5)) + print(fit) + + + ############################################################ + # Lines in three-dimensions + ############################################################ + x <- list(a=c(0,0,0), b=c(1,1,1)) # The 'diagonal' + y <- list(a=c(2,1,2), b=c(2,1,3)) # A 'fitted' line + fit <- distanceBetweenLines(ax=x$a, bx=x$b, ay=y$a, by=y$b) + + xlim <- ylim <- zlim <- c(-1,3) + dummy <- t(c(1,1,1))*100 + + # Coordinates for the lines in 3d + v <- seq(-10,10, by=1) + xv <- list(x=x$a[1]+x$b[1]*v, y=x$a[2]+x$b[2]*v, z=x$a[3]+x$b[3]*v) + yv <- list(x=y$a[1]+y$b[1]*v, y=y$a[2]+y$b[2]*v, z=y$a[3]+y$b[3]*v) + + for (theta in seq(30,140,length.out=3)) { + plot3d(dummy, theta=theta, phi=30, xlab="", ylab="", zlab="", + xlim=ylim, ylim=ylim, zlim=zlim) + + # Highlight the offset coordinates for both lines + points3d(t(x$a), pch="+", col="red") + text3d(t(x$a), label=expression(a[x]), adj=c(-1,0.5)) + points3d(t(y$a), pch="+", col="blue") + text3d(t(y$a), label=expression(a[y]), adj=c(-1,0.5)) + + # Draw the lines + lines3d(xv, col="red") + lines3d(yv, col="blue") + + # Draw the two points that are closest to each other + points3d(t(fit$xs), cex=2.0, col="red") + text3d(t(fit$xs), label=expression(x(s)), adj=c(+2,0.5)) + points3d(t(fit$yt), cex=1.5, col="blue") + text3d(t(fit$yt), label=expression(y(t)), adj=c(-1,0.5)) + + # Draw the distance between the two points + lines3d(rbind(fit$xs,fit$yt), col="purple", lwd=2) + } + + print(fit) + + } # for (zzz in 0) Loading required package: R.basic Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'R.basic' > rm(zzz) > > proc.time() user system elapsed 0.777 0.149 0.912
aroma.light.Rcheck/tests/findPeaksAndValleys.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > layout(matrix(1:3, ncol=1)) > par(mar=c(2,4,4,1)+0.1) > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # A unimodal distribution > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > x1 <- rnorm(n=10000, mean=0, sd=1) > x <- x1 > fit <- findPeaksAndValleys(x) > print(fit) type x density 1 peak -3.419149 1.312940e-03 2 valley -3.350202 1.310226e-03 3 peak -0.264852 4.005090e-01 4 valley 3.527199 6.273855e-05 5 peak 4.113243 5.936879e-04 > plot(density(x), lwd=2, main="x1") > abline(v=fit$x) > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # A trimodal distribution > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > x2 <- rnorm(n=10000, mean=4, sd=1) > x3 <- rnorm(n=10000, mean=8, sd=1) > x <- c(x1,x2,x3) > fit <- findPeaksAndValleys(x) > print(fit) type x density 1 peak -0.1109775 0.12454946 2 valley 2.0006589 0.04231170 3 peak 3.9691336 0.12477328 4 valley 5.9733987 0.04343636 5 peak 7.9776638 0.12503550 > plot(density(x), lwd=2, main="c(x1,x2,x3)") > abline(v=fit$x) > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # A trimodal distribution with clear separation > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - > x1b <- rnorm(n=10000, mean=0, sd=0.1) > x2b <- rnorm(n=10000, mean=4, sd=0.1) > x3b <- rnorm(n=10000, mean=8, sd=0.1) > x <- c(x1b,x2b,x3b) > > # Illustrating explicit usage of density() > d <- density(x) > fit <- findPeaksAndValleys(d, tol=0) > print(fit) type x density 1 peak -0.03195014 3.421131e-01 2 valley 1.98584741 1.135645e-06 3 peak 3.98217903 3.426521e-01 4 valley 5.97851064 1.199001e-06 5 peak 7.97484226 3.425314e-01 > plot(d, lwd=2, main="c(x1b,x2b,x3b)") > abline(v=fit$x) > > proc.time() user system elapsed 0.651 0.151 0.779
aroma.light.Rcheck/tests/fitPrincipalCurve.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Simulate data from the model y <- a + bx + x^c + eps(bx) > J <- 1000 > x <- rexp(J) > a <- c(2,15,3) > b <- c(2,3,4) > c <- c(1,2,1/2) > bx <- outer(b,x) > xc <- t(sapply(c, FUN=function(c) x^c)) > eps <- apply(bx, MARGIN=2, FUN=function(x) rnorm(length(b), mean=0, sd=0.1*x)) > y <- a + bx + xc + eps > y <- t(y) > > # Fit principal curve through (y_1, y_2, y_3) > fit <- fitPrincipalCurve(y, verbose=TRUE) Fitting principal curve... Data size: 1000x3 Identifying missing values... Identifying missing values...done Data size after removing non-finite data points: 1000x3 Calling principal_curve()... Starting curve---distance^2: 2654922 Iteration 1---distance^2: 429.0339 Iteration 2---distance^2: 427.6356 Iteration 3---distance^2: 427.6487 Converged: TRUE Number of iterations: 3 Processing time/iteration: 0.3s (0.1s/iteration) Calling principal_curve()...done Fitting principal curve...done > > # Flip direction of 'lambda'? > rho <- cor(fit$lambda, y[,1], use="complete.obs") > flip <- (rho < 0) > if (flip) { + fit$lambda <- max(fit$lambda, na.rm=TRUE)-fit$lambda + } > > > # Backtransform (y_1, y_2, y_3) to be proportional to each other > yN <- backtransformPrincipalCurve(y, fit=fit) > > # Same backtransformation dimension by dimension > yN2 <- y > for (cc in 1:ncol(y)) { + yN2[,cc] <- backtransformPrincipalCurve(y, fit=fit, dimensions=cc) + } > stopifnot(identical(yN2, yN)) > > > xlim <- c(0, 1.04*max(x)) > ylim <- range(c(y,yN), na.rm=TRUE) > > > # Pairwise signals vs x before and after transform > layout(matrix(1:4, nrow=2, byrow=TRUE)) > par(mar=c(4,4,3,2)+0.1) > for (cc in 1:3) { + ylab <- substitute(y[c], env=list(c=cc)) + plot(NA, xlim=xlim, ylim=ylim, xlab="x", ylab=ylab) + abline(h=a[cc], lty=3) + mtext(side=4, at=a[cc], sprintf("a=%g", a[cc]), + cex=0.8, las=2, line=0, adj=1.1, padj=-0.2) + points(x, y[,cc]) + points(x, yN[,cc], col="tomato") + legend("topleft", col=c("black", "tomato"), pch=19, + c("orignal", "transformed"), bty="n") + } > title(main="Pairwise signals vs x before and after transform", outer=TRUE, line=-2) > > > # Pairwise signals before and after transform > layout(matrix(1:4, nrow=2, byrow=TRUE)) > par(mar=c(4,4,3,2)+0.1) > for (rr in 3:2) { + ylab <- substitute(y[c], env=list(c=rr)) + for (cc in 1:2) { + if (cc == rr) { + plot.new() + next + } + xlab <- substitute(y[c], env=list(c=cc)) + plot(NA, xlim=ylim, ylim=ylim, xlab=xlab, ylab=ylab) + abline(a=0, b=1, lty=2) + points(y[,c(cc,rr)]) + points(yN[,c(cc,rr)], col="tomato") + legend("topleft", col=c("black", "tomato"), pch=19, + c("orignal", "transformed"), bty="n") + } + } > title(main="Pairwise signals before and after transform", outer=TRUE, line=-2) > > proc.time() user system elapsed 1.783 0.225 2.068
aroma.light.Rcheck/tests/fitXYCurve.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Simulate data from the model y <- a + bx + x^c + eps(bx) > x <- rexp(1000) > a <- c(2,15) > b <- c(2,1) > c <- c(1,2) > bx <- outer(b,x) > xc <- t(sapply(c, FUN=function(c) x^c)) > eps <- apply(bx, MARGIN=2, FUN=function(x) rnorm(length(x), mean=0, sd=0.1*x)) > Y <- a + bx + xc + eps > Y <- t(Y) > > lim <- c(0,70) > plot(Y, xlim=lim, ylim=lim) > > # Fit principal curve through a subset of (y_1, y_2) > subset <- sample(nrow(Y), size=0.3*nrow(Y)) > fit <- fitXYCurve(Y[subset,], bandwidth=0.2) > > lines(fit, col="red", lwd=2) > > # Backtransform (y_1, y_2) keeping y_1 unchanged > YN <- backtransformXYCurve(Y, fit=fit) > points(YN, col="blue") > abline(a=0, b=1, col="red", lwd=2) > > proc.time() user system elapsed 0.721 0.158 0.886
aroma.light.Rcheck/tests/iwpca.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > for (zzz in 0) { + + # This example requires plot3d() in R.basic [http://www.braju.com/R/] + if (!require(pkgName <- "R.basic", character.only=TRUE)) break + + # Simulate data from the model y <- a + bx + eps(bx) + x <- rexp(1000) + a <- c(2,15,3) + b <- c(2,3,4) + bx <- outer(b,x) + eps <- apply(bx, MARGIN=2, FUN=function(x) rnorm(length(x), mean=0, sd=0.1*x)) + y <- a + bx + eps + y <- t(y) + + # Add some outliers by permuting the dimensions for 1/10 of the observations + idx <- sample(1:nrow(y), size=1/10*nrow(y)) + y[idx,] <- y[idx,c(2,3,1)] + + # Plot the data with fitted lines at four different view points + opar <- par(mar=c(1,1,1,1)+0.1) + N <- 4 + layout(matrix(1:N, nrow=2, byrow=TRUE)) + theta <- seq(0,270,length.out=N) + phi <- rep(20, length.out=N) + xlim <- ylim <- zlim <- c(0,45) + persp <- list() + for (kk in seq_along(theta)) { + # Plot the data + persp[[kk]] <- plot3d(y, theta=theta[kk], phi=phi[kk], xlim=xlim, ylim=ylim, zlim=zlim) + } + + # Weights on the observations + # Example a: Equal weights + w <- NULL + # Example b: More weight on the outliers (uncomment to test) + w <- rep(1, length(x)); w[idx] <- 0.8 + + # ...and show all iterations too with different colors. + maxIter <- c(seq(1,20,length.out=10),Inf) + col <- topo.colors(length(maxIter)) + # Show the fitted value for every iteration + for (ii in seq_along(maxIter)) { + # Fit a line using IWPCA through data + fit <- iwpca(y, w=w, maxIter=maxIter[ii], swapDirections=TRUE) + + ymid <- fit$xMean + d0 <- apply(y, MARGIN=2, FUN=min) - ymid + d1 <- apply(y, MARGIN=2, FUN=max) - ymid + b <- fit$vt[1,] + y0 <- -b * max(abs(d0)) + y1 <- b * max(abs(d1)) + yline <- matrix(c(y0,y1), nrow=length(b), ncol=2) + yline <- yline + ymid + + for (kk in seq_along(theta)) { + # Set pane to draw in + par(mfg=c((kk-1) %/% 2, (kk-1) %% 2) + 1) + # Set the viewpoint of the pane + options(persp.matrix=persp[[kk]]) + + # Get the first principal component + points3d(t(ymid), col=col[ii]) + lines3d(t(yline), col=col[ii]) + + # Highlight the last one + if (ii == length(maxIter)) + lines3d(t(yline), col="red", lwd=3) + } + } + + par(opar) + + } # for (zzz in 0) Loading required package: R.basic Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'R.basic' > rm(zzz) > > proc.time() user system elapsed 0.714 0.147 0.852
aroma.light.Rcheck/tests/likelihood.smooth.spline.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Define f(x) > f <- expression(0.1*x^4 + 1*x^3 + 2*x^2 + x + 10*sin(2*x)) > > # Simulate data from this function in the range [a,b] > a <- -2; b <- 5 > x <- seq(a, b, length.out=3000) > y <- eval(f) > > # Add some noise to the data > y <- y + rnorm(length(y), 0, 10) > > # Plot the function and its second derivative > plot(x,y, type="l", lwd=4) > > # Fit a cubic smoothing spline and plot it > g <- smooth.spline(x,y, df=16) > lines(g, col="yellow", lwd=2, lty=2) > > # Calculating the (log) likelihood of the fitted spline > l <- likelihood(g) > > cat("Log likelihood with unique x values:\n") Log likelihood with unique x values: > print(l) Likelihood of smoothing spline: -308841 Log base: 2.718282 Weighted residuals sum of square: 308841.1 Penalty: -0.1184845 Smoothing parameter lambda: 0.0009257147 Roughness score: 127.9925 > > # Note that this is not the same as the log likelihood of the > # data on the fitted spline iff the x values are non-unique > x[1:5] <- x[1] # Non-unique x values > g <- smooth.spline(x,y, df=16) > l <- likelihood(g) > > cat("\nLog likelihood of the *spline* data set:\n") Log likelihood of the *spline* data set: > print(l) Likelihood of smoothing spline: -308371.9 Log base: 2.718282 Weighted residuals sum of square: 308372 Penalty: -0.1184963 Smoothing parameter lambda: 0.0009261969 Roughness score: 127.9385 > > # In cases with non unique x values one has to proceed as > # below if one want to get the log likelihood for the original > # data. > l <- likelihood(g, x=x, y=y) > cat("\nLog likelihood of the *original* data set:\n") Log likelihood of the *original* data set: > print(l) Likelihood of smoothing spline: -308842.2 Log base: 2.718282 Weighted residuals sum of square: 308842.3 Penalty: -0.1184963 Smoothing parameter lambda: 0.0009261969 Roughness score: 127.9385 > > > > > > > proc.time() user system elapsed 0.746 0.152 0.904
aroma.light.Rcheck/tests/medianPolish.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Deaths from sport parachuting; from ABC of EDA, p.224: > deaths <- matrix(c(14,15,14, 7,4,7, 8,2,10, 15,9,10, 0,2,0), ncol=3, byrow=TRUE) > rownames(deaths) <- c("1-24", "25-74", "75-199", "200++", "NA") > colnames(deaths) <- 1973:1975 > > print(deaths) 1973 1974 1975 1-24 14 15 14 25-74 7 4 7 75-199 8 2 10 200++ 15 9 10 NA 0 2 0 > > mp <- medianPolish(deaths) > mp1 <- medpolish(deaths, trace=FALSE) > print(mp) Median Polish Results (Dataset: "deaths") Overall: 8 Row Effects: 1-24 25-74 75-199 200++ NA 6 -1 0 2 -8 Column Effects: 1973 1974 1975 0 -1 0 Residuals: 1973 1974 1975 1-24 0 2 0 25-74 0 -2 0 75-199 0 -5 2 200++ 5 0 0 NA 0 3 0 > > ff <- c("overall", "row", "col", "residuals") > stopifnot(all.equal(mp[ff], mp1[ff])) > > # Validate decomposition: > stopifnot(all.equal(deaths, mp$overall+outer(mp$row,mp$col,"+")+mp$resid)) > > proc.time() user system elapsed 0.512 0.137 0.625
aroma.light.Rcheck/tests/normalizeAffine.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > pathname <- system.file("data-ex", "PMT-RGData.dat", package="aroma.light") > rg <- read.table(pathname, header=TRUE, sep="\t") > nbrOfScans <- max(rg$slide) > > rg <- as.list(rg) > for (field in c("R", "G")) + rg[[field]] <- matrix(as.double(rg[[field]]), ncol=nbrOfScans) > rg$slide <- rg$spot <- NULL > rg <- as.matrix(as.data.frame(rg)) > colnames(rg) <- rep(c("R", "G"), each=nbrOfScans) > > rgC <- rg > > layout(matrix(c(1,2,0,3,4,0,5,6,7), ncol=3, byrow=TRUE)) > > for (channel in c("R", "G")) { + sidx <- which(colnames(rg) == channel) + channelColor <- switch(channel, R="red", G="green") + + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # The raw data + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + plotMvsAPairs(rg, channel=channel) + title(main=paste("Observed", channel)) + box(col=channelColor) + + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # The calibrated data + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + rgC[,sidx] <- calibrateMultiscan(rg[,sidx], average=NULL) + + plotMvsAPairs(rgC, channel=channel) + title(main=paste("Calibrated", channel)) + box(col=channelColor) + } # for (channel ...) There were 50 or more warnings (use warnings() to see the first 50) > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # The average calibrated data > # > # Note how the red signals are weaker than the green. The reason > # for this can be that the scale factor in the green channel is > # greater than in the red channel, but it can also be that there > # is a remaining relative difference in bias between the green > # and the red channel, a bias that precedes the scanning. > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > rgCA <- matrix(NA_real_, nrow=nrow(rg), ncol=2) > colnames(rgCA) <- c("R", "G") > for (channel in c("R", "G")) { + sidx <- which(colnames(rg) == channel) + rgCA[,channel] <- calibrateMultiscan(rg[,sidx]) + } > > plotMvsA(rgCA) > title(main="Average calibrated") > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # The affine normalized average calibrated data > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Create a matrix where the columns represent the channels > # to be normalized. > rgCAN <- rgCA > # Affine normalization of channels > rgCAN <- normalizeAffine(rgCAN) > > plotMvsA(rgCAN) > title(main="Affine normalized A.C.") > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # It is always ok to rescale the affine normalized data if its > # done on (R,G); not on (A,M)! However, this is only needed for > # esthetic purposes. > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > rgCAN <- rgCAN * 2^5 > plotMvsA(rgCAN) > title(main="Rescaled normalized") > > > > proc.time() user system elapsed 4.550 0.338 5.095
aroma.light.Rcheck/tests/normalizeAverage.list.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Simulate ten samples of different lengths > N <- 10000 > X <- list() > for (kk in 1:8) { + rfcn <- list(rnorm, rgamma)[[sample(2, size=1)]] + size <- runif(1, min=0.3, max=1) + a <- rgamma(1, shape=20, rate=10) + b <- rgamma(1, shape=10, rate=10) + values <- rfcn(size*N, a, b) + + # "Censor" values + values[values < 0 | values > 8] <- NA_real_ + + X[[kk]] <- values + } > > # Add 20% missing values > X <- lapply(X, FUN=function(x) { + x[sample(length(x), size=0.20*length(x))] <- NA_real_ + x + }) > > # Normalize quantiles > Xn <- normalizeAverage(X, na.rm=TRUE, targetAvg=median(unlist(X), na.rm=TRUE)) > > # Plot the data > layout(matrix(1:2, ncol=1)) > xlim <- range(X, Xn, na.rm=TRUE) > plotDensity(X, lwd=2, xlim=xlim, main="The original distributions") > plotDensity(Xn, lwd=2, xlim=xlim, main="The normalized distributions") > > proc.time() user system elapsed 0.738 0.159 0.898
aroma.light.Rcheck/tests/normalizeAverage.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Simulate three samples with on average 20% missing values > N <- 10000 > X <- cbind(rnorm(N, mean=3, sd=1), + rnorm(N, mean=4, sd=2), + rgamma(N, shape=2, rate=1)) > X[sample(3*N, size=0.20*3*N)] <- NA_real_ > > # Normalize quantiles > Xn <- normalizeAverage(X, na.rm=TRUE, targetAvg=median(X, na.rm=TRUE)) > > # Plot the data > layout(matrix(1:2, ncol=1)) > xlim <- range(X, Xn, na.rm=TRUE) > plotDensity(X, lwd=2, xlim=xlim, main="The three original distributions") > plotDensity(Xn, lwd=2, xlim=xlim, main="The three normalized distributions") > > proc.time() user system elapsed 0.638 0.148 0.766
aroma.light.Rcheck/tests/normalizeCurveFit.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > pathname <- system.file("data-ex", "PMT-RGData.dat", package="aroma.light") > rg <- read.table(pathname, header=TRUE, sep="\t") > nbrOfScans <- max(rg$slide) > > rg <- as.list(rg) > for (field in c("R", "G")) + rg[[field]] <- matrix(as.double(rg[[field]]), ncol=nbrOfScans) > rg$slide <- rg$spot <- NULL > rg <- as.matrix(as.data.frame(rg)) > colnames(rg) <- rep(c("R", "G"), each=nbrOfScans) > > layout(matrix(c(1,2,0,3,4,0,5,6,7), ncol=3, byrow=TRUE)) > > rgC <- rg > for (channel in c("R", "G")) { + sidx <- which(colnames(rg) == channel) + channelColor <- switch(channel, R="red", G="green") + + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # The raw data + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + plotMvsAPairs(rg[,sidx]) + title(main=paste("Observed", channel)) + box(col=channelColor) + + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + # The calibrated data + # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + rgC[,sidx] <- calibrateMultiscan(rg[,sidx], average=NULL) + + plotMvsAPairs(rgC[,sidx]) + title(main=paste("Calibrated", channel)) + box(col=channelColor) + } # for (channel ...) > > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # The average calibrated data > # > # Note how the red signals are weaker than the green. The reason > # for this can be that the scale factor in the green channel is > # greater than in the red channel, but it can also be that there > # is a remaining relative difference in bias between the green > # and the red channel, a bias that precedes the scanning. > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > rgCA <- rg > for (channel in c("R", "G")) { + sidx <- which(colnames(rg) == channel) + rgCA[,sidx] <- calibrateMultiscan(rg[,sidx]) + } > > rgCAavg <- matrix(NA_real_, nrow=nrow(rgCA), ncol=2) > colnames(rgCAavg) <- c("R", "G") > for (channel in c("R", "G")) { + sidx <- which(colnames(rg) == channel) + rgCAavg[,channel] <- apply(rgCA[,sidx], MARGIN=1, FUN=median, na.rm=TRUE) + } > > # Add some "fake" outliers > outliers <- 1:600 > rgCAavg[outliers,"G"] <- 50000 > > plotMvsA(rgCAavg) > title(main="Average calibrated (AC)") > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Normalize data > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Weight-down outliers when normalizing > weights <- rep(1, nrow(rgCAavg)) > weights[outliers] <- 0.001 > > # Affine normalization of channels > rgCANa <- normalizeAffine(rgCAavg, weights=weights) > # It is always ok to rescale the affine normalized data if its > # done on (R,G); not on (A,M)! However, this is only needed for > # esthetic purposes. > rgCANa <- rgCANa *2^1.4 > plotMvsA(rgCANa) > title(main="Normalized AC") > > # Curve-fit (lowess) normalization > rgCANlw <- normalizeLowess(rgCAavg, weights=weights) Warning message: In normalizeCurveFit.matrix(X, method = "lowess", ...) : Weights were rounded to {0,1} since 'lowess' normalization supports only zero-one weights. > plotMvsA(rgCANlw, col="orange", add=TRUE) > > # Curve-fit (loess) normalization > rgCANl <- normalizeLoess(rgCAavg, weights=weights) > plotMvsA(rgCANl, col="red", add=TRUE) > > # Curve-fit (robust spline) normalization > rgCANrs <- normalizeRobustSpline(rgCAavg, weights=weights) > plotMvsA(rgCANrs, col="blue", add=TRUE) > > legend(x=0,y=16, legend=c("affine", "lowess", "loess", "r. spline"), pch=19, + col=c("black", "orange", "red", "blue"), ncol=2, x.intersp=0.3, bty="n") > > > plotMvsMPairs(cbind(rgCANa, rgCANlw), col="orange", xlab=expression(M[affine])) > title(main="Normalized AC") > plotMvsMPairs(cbind(rgCANa, rgCANl), col="red", add=TRUE) > plotMvsMPairs(cbind(rgCANa, rgCANrs), col="blue", add=TRUE) > abline(a=0, b=1, lty=2) > legend(x=-6,y=6, legend=c("lowess", "loess", "r. spline"), pch=19, + col=c("orange", "red", "blue"), ncol=2, x.intersp=0.3, bty="n") > > > proc.time() user system elapsed 12.708 0.334 13.849
aroma.light.Rcheck/tests/normalizeDifferencesToAverage.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Simulate three shifted tracks of different lengths with same profiles > ns <- c(A=2, B=1, C=0.25)*1000 > xx <- lapply(ns, FUN=function(n) { seq(from=1, to=max(ns), length.out=n) }) > zz <- mapply(seq_along(ns), ns, FUN=function(z,n) rep(z,n)) > > yy <- list( + A = rnorm(ns["A"], mean=0, sd=0.5), + B = rnorm(ns["B"], mean=5, sd=0.4), + C = rnorm(ns["C"], mean=-5, sd=1.1) + ) > yy <- lapply(yy, FUN=function(y) { + n <- length(y) + y[1:(n/2)] <- y[1:(n/2)] + 2 + y[1:(n/4)] <- y[1:(n/4)] - 4 + y + }) > > # Shift all tracks toward the first track > yyN <- normalizeDifferencesToAverage(yy, baseline=1) > > # The baseline channel is not changed > stopifnot(identical(yy[[1]], yyN[[1]])) > > # Get the estimated parameters > fit <- attr(yyN, "fit") > > # Plot the tracks > layout(matrix(1:2, ncol=1)) > x <- unlist(xx) > col <- unlist(zz) > y <- unlist(yy) > yN <- unlist(yyN) > plot(x, y, col=col, ylim=c(-10,10)) > plot(x, yN, col=col, ylim=c(-10,10)) > > proc.time() user system elapsed 0.762 0.169 0.938
aroma.light.Rcheck/tests/normalizeFragmentLength-ex1.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Example 1: Single-enzyme fragment-length normalization of 6 arrays > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Number samples > I <- 9 > > # Number of loci > J <- 1000 > > # Fragment lengths > fl <- seq(from=100, to=1000, length.out=J) > > # Simulate data points with unknown fragment lengths > hasUnknownFL <- seq(from=1, to=J, by=50) > fl[hasUnknownFL] <- NA_real_ > > # Simulate data > y <- matrix(0, nrow=J, ncol=I) > maxY <- 12 > for (kk in 1:I) { + k <- runif(n=1, min=3, max=5) + mu <- function(fl) { + mu <- rep(maxY, length(fl)) + ok <- !is.na(fl) + mu[ok] <- mu[ok] - fl[ok]^{1/k} + mu + } + eps <- rnorm(J, mean=0, sd=1) + y[,kk] <- mu(fl) + eps + } > > # Normalize data (to a zero baseline) > yN <- apply(y, MARGIN=2, FUN=function(y) { + normalizeFragmentLength(y, fragmentLengths=fl, onMissing="median") + }) > > # The correction factors > rho <- y-yN > print(summary(rho)) V1 V2 V3 V4 Min. :3.105 Min. :7.283 Min. :5.630 Min. :5.729 1st Qu.:3.968 1st Qu.:7.695 1st Qu.:6.189 1st Qu.:6.100 Median :4.845 Median :8.089 Median :6.771 Median :6.556 Mean :5.030 Mean :8.107 Mean :6.875 Mean :6.728 3rd Qu.:6.047 3rd Qu.:8.501 3rd Qu.:7.523 3rd Qu.:7.307 Max. :7.524 Max. :9.030 Max. :8.497 Max. :8.298 V5 V6 V7 V8 Min. :7.009 Min. :5.691 Min. :3.609 Min. :5.673 1st Qu.:7.342 1st Qu.:6.178 1st Qu.:4.373 1st Qu.:6.183 Median :7.681 Median :6.723 Median :5.138 Median :6.690 Mean :7.786 Mean :6.824 Mean :5.285 Mean :6.844 3rd Qu.:8.199 3rd Qu.:7.430 3rd Qu.:6.172 3rd Qu.:7.455 Max. :8.918 Max. :8.337 Max. :7.385 Max. :8.540 V9 Min. :3.407 1st Qu.:4.125 Median :4.930 Mean :5.111 3rd Qu.:6.038 Max. :7.440 > # The correction for units with unknown fragment lengths > # equals the median correction factor of all other units > print(summary(rho[hasUnknownFL,])) V1 V2 V3 V4 Min. :4.845 Min. :8.089 Min. :6.771 Min. :6.556 1st Qu.:4.845 1st Qu.:8.089 1st Qu.:6.771 1st Qu.:6.556 Median :4.845 Median :8.089 Median :6.771 Median :6.556 Mean :4.845 Mean :8.089 Mean :6.771 Mean :6.556 3rd Qu.:4.845 3rd Qu.:8.089 3rd Qu.:6.771 3rd Qu.:6.556 Max. :4.845 Max. :8.089 Max. :6.771 Max. :6.556 V5 V6 V7 V8 V9 Min. :7.681 Min. :6.723 Min. :5.138 Min. :6.69 Min. :4.93 1st Qu.:7.681 1st Qu.:6.723 1st Qu.:5.138 1st Qu.:6.69 1st Qu.:4.93 Median :7.681 Median :6.723 Median :5.138 Median :6.69 Median :4.93 Mean :7.681 Mean :6.723 Mean :5.138 Mean :6.69 Mean :4.93 3rd Qu.:7.681 3rd Qu.:6.723 3rd Qu.:5.138 3rd Qu.:6.69 3rd Qu.:4.93 Max. :7.681 Max. :6.723 Max. :5.138 Max. :6.69 Max. :4.93 > > # Plot raw data > layout(matrix(1:9, ncol=3)) > xlim <- c(0,max(fl, na.rm=TRUE)) > ylim <- c(0,max(y, na.rm=TRUE)) > xlab <- "Fragment length" > ylab <- expression(log2(theta)) > for (kk in 1:I) { + plot(fl, y[,kk], xlim=xlim, ylim=ylim, xlab=xlab, ylab=ylab) + ok <- (is.finite(fl) & is.finite(y[,kk])) + lines(lowess(fl[ok], y[ok,kk]), col="red", lwd=2) + } > > # Plot normalized data > layout(matrix(1:9, ncol=3)) > ylim <- c(-1,1)*max(y, na.rm=TRUE)/2 > for (kk in 1:I) { + plot(fl, yN[,kk], xlim=xlim, ylim=ylim, xlab=xlab, ylab=ylab) + ok <- (is.finite(fl) & is.finite(y[,kk])) + lines(lowess(fl[ok], yN[ok,kk]), col="blue", lwd=2) + } > > proc.time() user system elapsed 1.481 0.215 1.754
aroma.light.Rcheck/tests/normalizeFragmentLength-ex2.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # Example 2: Two-enzyme fragment-length normalization of 6 arrays > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > set.seed(0xbeef) > > # Number samples > I <- 5 > > # Number of loci > J <- 3000 > > # Fragment lengths (two enzymes) > fl <- matrix(0, nrow=J, ncol=2) > fl[,1] <- seq(from=100, to=1000, length.out=J) > fl[,2] <- seq(from=1000, to=100, length.out=J) > > # Let 1/2 of the units be on both enzymes > fl[seq(from=1, to=J, by=4),1] <- NA_real_ > fl[seq(from=2, to=J, by=4),2] <- NA_real_ > > # Let some have unknown fragment lengths > hasUnknownFL <- seq(from=1, to=J, by=15) > fl[hasUnknownFL,] <- NA_real_ > > # Sty/Nsp mixing proportions: > rho <- rep(1, I) > rho[1] <- 1/3; # Less Sty in 1st sample > rho[3] <- 3/2; # More Sty in 3rd sample > > > # Simulate data > z <- array(0, dim=c(J,2,I)) > maxLog2Theta <- 12 > for (ii in 1:I) { + # Common effect for both enzymes + mu <- function(fl) { + k <- runif(n=1, min=3, max=5) + mu <- rep(maxLog2Theta, length(fl)) + ok <- is.finite(fl) + mu[ok] <- mu[ok] - fl[ok]^{1/k} + mu + } + + # Calculate the effect for each data point + for (ee in 1:2) { + z[,ee,ii] <- mu(fl[,ee]) + } + + # Update the Sty/Nsp mixing proportions + ee <- 2 + z[,ee,ii] <- rho[ii]*z[,ee,ii] + + # Add random errors + for (ee in 1:2) { + eps <- rnorm(J, mean=0, sd=1/sqrt(2)) + z[,ee,ii] <- z[,ee,ii] + eps + } + } > > > hasFl <- is.finite(fl) > > unitSets <- list( + nsp = which( hasFl[,1] & !hasFl[,2]), + sty = which(!hasFl[,1] & hasFl[,2]), + both = which( hasFl[,1] & hasFl[,2]), + none = which(!hasFl[,1] & !hasFl[,2]) + ) > > # The observed data is a mix of two enzymes > theta <- matrix(NA_real_, nrow=J, ncol=I) > > # Single-enzyme units > for (ee in 1:2) { + uu <- unitSets[[ee]] + theta[uu,] <- 2^z[uu,ee,] + } > > # Both-enzyme units (sum on intensity scale) > uu <- unitSets$both > theta[uu,] <- (2^z[uu,1,]+2^z[uu,2,])/2 > > # Missing units (sample from the others) > uu <- unitSets$none > theta[uu,] <- apply(theta, MARGIN=2, sample, size=length(uu)) > > # Calculate target array > thetaT <- rowMeans(theta, na.rm=TRUE) > targetFcns <- list() > for (ee in 1:2) { + uu <- unitSets[[ee]] + fit <- lowess(fl[uu,ee], log2(thetaT[uu])) + class(fit) <- "lowess" + targetFcns[[ee]] <- function(fl, ...) { + predict(fit, newdata=fl) + } + } > > > # Fit model only to a subset of the data > subsetToFit <- setdiff(1:J, seq(from=1, to=J, by=10)) > > # Normalize data (to a target baseline) > thetaN <- matrix(NA_real_, nrow=J, ncol=I) > fits <- vector("list", I) > for (ii in 1:I) { + lthetaNi <- normalizeFragmentLength(log2(theta[,ii]), targetFcns=targetFcns, + fragmentLengths=fl, onMissing="median", + subsetToFit=subsetToFit, .returnFit=TRUE) + fits[[ii]] <- attr(lthetaNi, "modelFit") + thetaN[,ii] <- 2^lthetaNi + } > > > # Plot raw data > xlim <- c(0, max(fl, na.rm=TRUE)) > ylim <- c(0, max(log2(theta), na.rm=TRUE)) > Mlim <- c(-1,1)*4 > xlab <- "Fragment length" > ylab <- expression(log2(theta)) > Mlab <- expression(M==log[2](theta/theta[R])) > > layout(matrix(1:(3*I), ncol=I, byrow=TRUE)) > for (ii in 1:I) { + plot(NA, xlim=xlim, ylim=ylim, xlab=xlab, ylab=ylab, main="raw") + + # Single-enzyme units + for (ee in 1:2) { + # The raw data + uu <- unitSets[[ee]] + points(fl[uu,ee], log2(theta[uu,ii]), col=ee+1) + } + + # Both-enzyme units (use fragment-length for enzyme #1) + uu <- unitSets$both + points(fl[uu,1], log2(theta[uu,ii]), col=3+1) + + for (ee in 1:2) { + # The true effects + uu <- unitSets[[ee]] + lines(lowess(fl[uu,ee], log2(theta[uu,ii])), col="black", lwd=4, lty=3) + + # The estimated effects + fit <- fits[[ii]][[ee]]$fit + lines(fit, col="orange", lwd=3) + + muT <- targetFcns[[ee]](fl[uu,ee]) + lines(fl[uu,ee], muT, col="cyan", lwd=1) + } + } > > # Calculate log-ratios > thetaR <- rowMeans(thetaN, na.rm=TRUE) > M <- log2(thetaN/thetaR) > > # Plot normalized data > for (ii in 1:I) { + plot(NA, xlim=xlim, ylim=Mlim, xlab=xlab, ylab=Mlab, main="normalized") + # Single-enzyme units + for (ee in 1:2) { + # The normalized data + uu <- unitSets[[ee]] + points(fl[uu,ee], M[uu,ii], col=ee+1) + } + # Both-enzyme units (use fragment-length for enzyme #1) + uu <- unitSets$both + points(fl[uu,1], M[uu,ii], col=3+1) + } > > ylim <- c(0,1.5) > for (ii in 1:I) { + data <- list() + for (ee in 1:2) { + # The normalized data + uu <- unitSets[[ee]] + data[[ee]] <- M[uu,ii] + } + uu <- unitSets$both + if (length(uu) > 0) + data[[3]] <- M[uu,ii] + + uu <- unitSets$none + if (length(uu) > 0) + data[[4]] <- M[uu,ii] + + cols <- seq_along(data)+1 + plotDensity(data, col=cols, xlim=Mlim, xlab=Mlab, main="normalized") + + abline(v=0, lty=2) + } > > > proc.time() user system elapsed 1.412 0.239 1.687
aroma.light.Rcheck/tests/normalizeQuantileRank.list.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Simulate ten samples of different lengths > N <- 10000 > X <- list() > for (kk in 1:8) { + rfcn <- list(rnorm, rgamma)[[sample(2, size=1)]] + size <- runif(1, min=0.3, max=1) + a <- rgamma(1, shape=20, rate=10) + b <- rgamma(1, shape=10, rate=10) + values <- rfcn(size*N, a, b) + + # "Censor" values + values[values < 0 | values > 8] <- NA_real_ + + X[[kk]] <- values + } > > # Add 20% missing values > X <- lapply(X, FUN=function(x) { + x[sample(length(x), size=0.20*length(x))] <- NA_real_ + x + }) > > # Normalize quantiles > Xn <- normalizeQuantile(X) > > # Plot the data > layout(matrix(1:2, ncol=1)) > xlim <- range(X, na.rm=TRUE) > plotDensity(X, lwd=2, xlim=xlim, main="The original distributions") > plotDensity(Xn, lwd=2, xlim=xlim, main="The normalized distributions") > > proc.time() user system elapsed 0.782 0.167 0.933
aroma.light.Rcheck/tests/normalizeQuantileRank.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Simulate three samples with on average 20% missing values > N <- 10000 > X <- cbind(rnorm(N, mean=3, sd=1), + rnorm(N, mean=4, sd=2), + rgamma(N, shape=2, rate=1)) > X[sample(3*N, size=0.20*3*N)] <- NA_real_ > > # Normalize quantiles > Xn <- normalizeQuantile(X) > > # Plot the data > layout(matrix(1:2, ncol=1)) > xlim <- range(X, Xn, na.rm=TRUE) > plotDensity(X, lwd=2, xlim=xlim, main="The three original distributions") > plotDensity(Xn, lwd=2, xlim=xlim, main="The three normalized distributions") > > proc.time() user system elapsed 0.643 0.154 0.779
aroma.light.Rcheck/tests/normalizeQuantileSpline.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Simulate three samples with on average 20% missing values > N <- 10000 > X <- cbind(rnorm(N, mean=3, sd=1), + rnorm(N, mean=4, sd=2), + rgamma(N, shape=2, rate=1)) > X[sample(3*N, size=0.20*3*N)] <- NA_real_ > > # Plot the data > layout(matrix(c(1,0,2:5), ncol=2, byrow=TRUE)) > xlim <- range(X, na.rm=TRUE) > plotDensity(X, lwd=2, xlim=xlim, main="The three original distributions") > > Xn <- normalizeQuantile(X) > plotDensity(Xn, lwd=2, xlim=xlim, main="The three normalized distributions") > plotXYCurve(X, Xn, xlim=xlim, main="The three normalized distributions") > > Xn2 <- normalizeQuantileSpline(X, xTarget=Xn[,1], spar=0.99) > plotDensity(Xn2, lwd=2, xlim=xlim, main="The three normalized distributions") > plotXYCurve(X, Xn2, xlim=xlim, main="The three normalized distributions") > > proc.time() user system elapsed 1.680 0.249 1.993
aroma.light.Rcheck/tests/normalizeTumorBoost,flavors.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > library("R.utils") Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help. R.oo v1.27.0 (2024-11-01 18:00:02 UTC) successfully loaded. See ?R.oo for help. Attaching package: 'R.oo' The following object is masked from 'package:R.methodsS3': throw The following objects are masked from 'package:methods': getClasses, getMethods The following objects are masked from 'package:base': attach, detach, load, save R.utils v2.13.0 (2025-02-24 21:20:02 UTC) successfully loaded. See ?R.utils for help. Attaching package: 'R.utils' The following object is masked from 'package:utils': timestamp The following objects are masked from 'package:base': cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings > > # Load data > pathname <- system.file("data-ex/TumorBoost,fracB,exampleData.Rbin", package="aroma.light") > data <- loadObject(pathname) > > # Drop loci with missing values > data <- na.omit(data) > > attachLocally(data) > pos <- position/1e6 > > # Call naive genotypes > muN <- callNaiveGenotypes(betaN) > > # Genotype classes > isAA <- (muN == 0) > isAB <- (muN == 1/2) > isBB <- (muN == 1) > > # Sanity checks > stopifnot(all(muN[isAA] == 0)) > stopifnot(all(muN[isAB] == 1/2)) > stopifnot(all(muN[isBB] == 1)) > > # TumorBoost normalization with different flavors > betaTNs <- list() > for (flavor in c("v1", "v2", "v3", "v4")) { + betaTN <- normalizeTumorBoost(betaT=betaT, betaN=betaN, preserveScale=FALSE, flavor=flavor) + + # Assert that no non-finite values are introduced + stopifnot(all(is.finite(betaTN))) + + # Assert that nothing is flipped + stopifnot(all(betaTN[isAA] < 1/2)) + stopifnot(all(betaTN[isBB] > 1/2)) + + betaTNs[[flavor]] <- betaTN + } > > # Plot > layout(matrix(1:4, ncol=1)) > par(mar=c(2.5,4,0.5,1)+0.1) > ylim <- c(-0.05, 1.05) > col <- rep("#999999", length(muN)) > col[muN == 1/2] <- "#000000" > for (flavor in names(betaTNs)) { + betaTN <- betaTNs[[flavor]] + ylab <- sprintf("betaTN[%s]", flavor) + plot(pos, betaTN, col=col, ylim=ylim, ylab=ylab) + } > > proc.time() user system elapsed 1.040 0.208 1.258
aroma.light.Rcheck/tests/normalizeTumorBoost.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > library("R.utils") Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help. R.oo v1.27.0 (2024-11-01 18:00:02 UTC) successfully loaded. See ?R.oo for help. Attaching package: 'R.oo' The following object is masked from 'package:R.methodsS3': throw The following objects are masked from 'package:methods': getClasses, getMethods The following objects are masked from 'package:base': attach, detach, load, save R.utils v2.13.0 (2025-02-24 21:20:02 UTC) successfully loaded. See ?R.utils for help. Attaching package: 'R.utils' The following object is masked from 'package:utils': timestamp The following objects are masked from 'package:base': cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings > > # Load data > pathname <- system.file("data-ex/TumorBoost,fracB,exampleData.Rbin", package="aroma.light") > data <- loadObject(pathname) > attachLocally(data) > pos <- position/1e6 > muN <- genotypeN > > layout(matrix(1:4, ncol=1)) > par(mar=c(2.5,4,0.5,1)+0.1) > ylim <- c(-0.05, 1.05) > col <- rep("#999999", length(muN)) > col[muN == 1/2] <- "#000000" > > # Allele B fractions for the normal sample > plot(pos, betaN, col=col, ylim=ylim) > > # Allele B fractions for the tumor sample > plot(pos, betaT, col=col, ylim=ylim) > > # TumorBoost w/ naive genotype calls > betaTN <- normalizeTumorBoost(betaT=betaT, betaN=betaN, preserveScale=FALSE) > plot(pos, betaTN, col=col, ylim=ylim) > > # TumorBoost w/ external multi-sample genotype calls > betaTNx <- normalizeTumorBoost(betaT=betaT, betaN=betaN, muN=muN, preserveScale=FALSE) > plot(pos, betaTNx, col=col, ylim=ylim) > > proc.time() user system elapsed 0.926 0.200 1.130
aroma.light.Rcheck/tests/robustSmoothSpline.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > data(cars) > attach(cars) > plot(speed, dist, main = "data(cars) & robust smoothing splines") > > # Fit a smoothing spline using L_2 norm > cars.spl <- smooth.spline(speed, dist) > lines(cars.spl, col = "blue") > > # Fit a smoothing spline using L_1 norm > cars.rspl <- robustSmoothSpline(speed, dist) > lines(cars.rspl, col = "red") > > # Fit a smoothing spline using L_2 norm with 10 degrees of freedom > lines(smooth.spline(speed, dist, df=10), lty=2, col = "blue") > > # Fit a smoothing spline using L_1 norm with 10 degrees of freedom > lines(robustSmoothSpline(speed, dist, df=10), lty=2, col = "red") > > # Fit a smoothing spline using Tukey's biweight norm > cars.rspl <- robustSmoothSpline(speed, dist, method = "symmetric") > lines(cars.rspl, col = "purple") > > legend(5,120, c( + paste("smooth.spline [C.V.] => df =",round(cars.spl$df,1)), + paste("robustSmoothSpline L1 [C.V.] => df =",round(cars.rspl$df,1)), + paste("robustSmoothSpline symmetric [C.V.] => df =",round(cars.rspl$df,1)), + "standard with s( * , df = 10)", "robust with s( * , df = 10)" + ), + col = c("blue","red","purple","blue","red"), lty = c(1,1,1,2,2), + bg='bisque') > > proc.time() user system elapsed 0.740 0.152 0.879
aroma.light.Rcheck/tests/rowAverages.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > X <- matrix(1:30, nrow=5L, ncol=6L) > mu <- rowMeans(X) > sd <- apply(X, MARGIN=1L, FUN=sd) > > y <- rowAverages(X) > stopifnot(all(y == mu)) > stopifnot(all(attr(y,"deviance") == sd)) > stopifnot(all(attr(y,"df") == ncol(X))) > > proc.time() user system elapsed 0.513 0.136 0.622
aroma.light.Rcheck/tests/sampleCorrelations.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # Simulate 20000 genes with 10 observations each > X <- matrix(rnorm(n=20000), ncol=10) > > # Calculate the correlation for 5000 random gene pairs > cor <- sampleCorrelations(X, npairs=5000) > print(summary(cor)) Min. 1st Qu. Median Mean 3rd Qu. Max. -0.9483486 -0.2415730 0.0002962 -0.0033861 0.2333316 0.8969635 > > > proc.time() user system elapsed 1.163 0.180 1.359
aroma.light.Rcheck/tests/sampleTuples.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > pairs <- sampleTuples(1:10, size=5, length=2) > print(pairs) [,1] [,2] [1,] 7 6 [2,] 8 1 [3,] 8 4 [4,] 7 10 [5,] 4 6 > > triples <- sampleTuples(1:10, size=5, length=3) > print(triples) [,1] [,2] [,3] [1,] 2 4 9 [2,] 1 10 2 [3,] 9 4 3 [4,] 7 4 2 [5,] 10 2 6 > > # Allow tuples with repeated elements > quadruples <- sampleTuples(1:3, size=5, length=4, replace=TRUE) > print(quadruples) [,1] [,2] [,3] [,4] [1,] 3 1 1 3 [2,] 2 1 1 3 [3,] 1 3 1 2 [4,] 2 3 2 2 [5,] 2 2 1 3 > > proc.time() user system elapsed 0.514 0.142 0.651
aroma.light.Rcheck/tests/wpca.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > for (zzz in 0) { + + # This example requires plot3d() in R.basic [http://www.braju.com/R/] + if (!require(pkgName <- "R.basic", character.only=TRUE)) break + + # ------------------------------------------------------------- + # A first example + # ------------------------------------------------------------- + # Simulate data from the model y <- a + bx + eps(bx) + x <- rexp(1000) + a <- c(2,15,3) + b <- c(2,3,15) + bx <- outer(b,x) + eps <- apply(bx, MARGIN=2, FUN=function(x) rnorm(length(x), mean=0, sd=0.1*x)) + y <- a + bx + eps + y <- t(y) + + # Add some outliers by permuting the dimensions for 1/3 of the observations + idx <- sample(1:nrow(y), size=1/3*nrow(y)) + y[idx,] <- y[idx,c(2,3,1)] + + # Down-weight the outliers W times to demonstrate how weights are used + W <- 10 + + # Plot the data with fitted lines at four different view points + N <- 4 + theta <- seq(0,180,length.out=N) + phi <- rep(30, length.out=N) + + # Use a different color for each set of weights + col <- topo.colors(W) + + opar <- par(mar=c(1,1,1,1)+0.1) + layout(matrix(1:N, nrow=2, byrow=TRUE)) + for (kk in seq(theta)) { + # Plot the data + plot3d(y, theta=theta[kk], phi=phi[kk]) + + # First, same weights for all observations + w <- rep(1, length=nrow(y)) + + for (ww in 1:W) { + # Fit a line using IWPCA through data + fit <- wpca(y, w=w, swapDirections=TRUE) + + # Get the first principal component + ymid <- fit$xMean + d0 <- apply(y, MARGIN=2, FUN=min) - ymid + d1 <- apply(y, MARGIN=2, FUN=max) - ymid + b <- fit$vt[1,] + y0 <- -b * max(abs(d0)) + y1 <- b * max(abs(d1)) + yline <- matrix(c(y0,y1), nrow=length(b), ncol=2) + yline <- yline + ymid + + points3d(t(ymid), col=col) + lines3d(t(yline), col=col) + + # Down-weight outliers only, because here we know which they are. + w[idx] <- w[idx]/2 + } + + # Highlight the last one + lines3d(t(yline), col="red", lwd=3) + } + + par(opar) + + } # for (zzz in 0) Loading required package: R.basic Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'R.basic' > rm(zzz) > > proc.time() user system elapsed 0.669 0.147 0.817
aroma.light.Rcheck/tests/wpca2.matrix.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("aroma.light") aroma.light v3.36.0 (2025-03-31) successfully loaded. See ?aroma.light for help. > > # ------------------------------------------------------------- > # A second example > # ------------------------------------------------------------- > # Data > x <- c(1,2,3,4,5) > y <- c(2,4,3,3,6) > > opar <- par(bty="L") > opalette <- palette(c("blue", "red", "black")) > xlim <- ylim <- c(0,6) > > # Plot the data and the center mass > plot(x,y, pch=16, cex=1.5, xlim=xlim, ylim=ylim) > points(mean(x), mean(y), cex=2, lwd=2, col="blue") > > > # Linear regression y ~ x > fit <- lm(y ~ x) > abline(fit, lty=1, col=1) > > # Linear regression y ~ x through without intercept > fit <- lm(y ~ x - 1) > abline(fit, lty=2, col=1) > > > # Linear regression x ~ y > fit <- lm(x ~ y) > c <- coefficients(fit) > b <- 1/c[2] > a <- -b*c[1] > abline(a=a, b=b, lty=1, col=2) > > # Linear regression x ~ y through without intercept > fit <- lm(x ~ y - 1) > b <- 1/coefficients(fit) > abline(a=0, b=b, lty=2, col=2) > > > # Orthogonal linear "regression" > fit <- wpca(cbind(x,y)) > > b <- fit$vt[1,2]/fit$vt[1,1] > a <- fit$xMean[2]-b*fit$xMean[1] > abline(a=a, b=b, lwd=2, col=3) > > # Orthogonal linear "regression" without intercept > fit <- wpca(cbind(x,y), center=FALSE) > b <- fit$vt[1,2]/fit$vt[1,1] > a <- fit$xMean[2]-b*fit$xMean[1] > abline(a=a, b=b, lty=2, lwd=2, col=3) > > legend(xlim[1],ylim[2], legend=c("lm(y~x)", "lm(y~x-1)", "lm(x~y)", + "lm(x~y-1)", "pca", "pca w/o intercept"), lty=rep(1:2,3), + lwd=rep(c(1,1,2),each=2), col=rep(1:3,each=2)) > > palette(opalette) > par(opar) > > proc.time() user system elapsed 0.625 0.146 0.756
aroma.light.Rcheck/aroma.light-Ex.timings
name | user | system | elapsed | |
backtransformAffine | 0.005 | 0.006 | 0.011 | |
backtransformPrincipalCurve | 0.923 | 0.050 | 1.082 | |
calibrateMultiscan | 0 | 0 | 0 | |
callNaiveGenotypes | 0.441 | 0.033 | 0.530 | |
distanceBetweenLines | 0.240 | 0.008 | 0.273 | |
findPeaksAndValleys | 0.055 | 0.006 | 0.072 | |
fitPrincipalCurve | 0.900 | 0.044 | 1.055 | |
fitXYCurve | 0.299 | 0.011 | 0.347 | |
iwpca | 0.152 | 0.004 | 0.169 | |
likelihood.smooth.spline | 0.212 | 0.008 | 0.239 | |
medianPolish | 0.010 | 0.002 | 0.015 | |
normalizeAffine | 11.917 | 0.163 | 13.247 | |
normalizeCurveFit | 12.156 | 0.155 | 13.316 | |
normalizeDifferencesToAverage | 0.368 | 0.034 | 0.443 | |
normalizeFragmentLength | 2.139 | 0.156 | 2.579 | |
normalizeQuantileRank | 1.206 | 0.030 | 1.315 | |
normalizeQuantileRank.matrix | 0.065 | 0.005 | 0.074 | |
normalizeQuantileSpline | 1.186 | 0.054 | 1.289 | |
normalizeTumorBoost | 0.373 | 0.047 | 0.441 | |
robustSmoothSpline | 0.597 | 0.018 | 0.654 | |
sampleCorrelations | 0.648 | 0.019 | 0.691 | |
sampleTuples | 0.001 | 0.001 | 0.002 | |
wpca | 0.148 | 0.008 | 0.165 | |