Man pages for HenrikBengtsson/aroma.light
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

1._Calibration_and_Normalization1. Calibration and Normalization
aroma.light-packagePackage aroma.light
averageQuantileGets the average empirical distribution
backtransformAffineReverse affine transformation
backtransformPrincipalCurveReverse transformation of principal-curve fit
calibrateMultiscanWeighted affine calibration of a multiple re-scanned channel
callNaiveGenotypesCalls genotypes in a normal sample
distanceBetweenLinesFinds the shortest distance between two lines
findPeaksAndValleysFinds extreme points in the empirical density estimated from...
fitIWPCARobust fit of linear subspace through multidimensional data
fitNaiveGenotypesFit naive genotype model from a normal sample
fitPrincipalCurveFit a principal curve in K dimensions
fitXYCurveFitting a smooth curve through paired (x,y) data
iwpcaFits an R-dimensional hyperplane using iterative re-weighted...
likelihood.smooth.splineCalculate the log likelihood of a smoothing spline given the...
medianPolishMedian polish
Non-documented_objectsNon-documented objects
normalizeAffineWeighted affine normalization between channels and arrays
normalizeAverageRescales channel vectors to get the same average
normalizeCurveFitWeighted curve-fit normalization between a pair of channels
normalizeDifferencesToAverageRescales channel vectors to get the same average
normalizeFragmentLengthNormalizes signals for PCR fragment-length effects
normalizeQuantileRankNormalizes the empirical distribution of one of more samples...
normalizeQuantileRank.matrixNormalizes the empirical distribution of a set of samples to...
normalizeQuantileSplineNormalizes the empirical distribution of one or more samples...
normalizeTumorBoostNormalizes allele B fractions for a tumor given a match...
pairedAlleleSpecificCopyNumbersCalculating tumor-normal paired allele-specific copy number...
plotDensityPlots density distributions for a set of vectors
plotMvsAPlot log-ratios vs log-intensities
plotMvsAPairsPlot log-ratios/log-intensities for all unique pairs of data...
plotMvsMPairsPlot log-ratios vs log-ratios for all pairs of columns
plotXYCurvePlot the relationship between two variables as a smooth curve
print.SmoothSplineLikelihoodPrints an SmoothSplineLikelihood object
robustSmoothSplineRobust fit of a Smoothing Spline
sampleCorrelationsCalculates the correlation for random pairs of observations
sampleTuplesSample tuples of elements from a set
wpcaLight-weight Weighted Principal Component Analysis
HenrikBengtsson/aroma.light documentation built on May 7, 2019, 1:56 a.m.