/usr/lib/R/site-library/aroma.light/INDEX is in r-bioc-aroma.light 3.0.0-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | 1. Calibration and Normalization
1. Calibration and Normalization
aroma.light-package Package aroma.light
averageQuantile Gets the average empirical distribution
backtransformAffine Reverse affine transformation
backtransformPrincipalCurve
Reverse transformation of principal-curve fit
calibrateMultiscan Weighted affine calibration of a multiple
re-scanned channel
callNaiveGenotypes Calls genotypes in a normal sample
distanceBetweenLines Finds the shortest distance between two lines
fitIWPCA Robust fit of linear subspace through
multidimensional data
fitNaiveGenotypes Fit naive genotype model from a normal sample
fitPrincipalCurve Fit a principal curve in K dimensions
fitXYCurve Fitting a smooth curve through paired (x,y)
data
iwpca Fits an R-dimensional hyperplane using
iterative re-weighted PCA
medianPolish Median polish
normalizeAffine Weighted affine normalization between channels
and arrays
normalizeAverage Rescales channel vectors to get the same
average
normalizeCurveFit Weighted curve-fit normalization between a pair
of channels
normalizeDifferencesToAverage
Rescales channel vectors to get the same
average
normalizeFragmentLength
Normalizes signals for PCR fragment-length
effects
normalizeQuantileRank Normalizes the empirical distribution of one of
more samples to a target distribution
normalizeQuantileRank.matrix
Normalizes the empirical distribution of a set
of samples to a common target distribution
normalizeQuantileSpline
Normalizes the empirical distribution of one or
more samples to a target distribution
normalizeTumorBoost Normalizes allele B fractions for a tumor given
a match normal
pairedAlleleSpecificCopyNumbers
Calculating tumor-normal paired allele-specific
copy number stratified on genotypes
plotDensity Plots density distributions for a set of
vectors
plotMvsA Plot log-ratios vs log-intensities
plotMvsAPairs Plot log-ratios/log-intensities for all unique
pairs of data vectors
plotMvsMPairs Plot log-ratios vs log-ratios for all pairs of
columns
plotXYCurve Plot the relationship between two variables as
a smooth curve
robustSmoothSpline Robust fit of a Smoothing Spline
sampleCorrelations Calculates the correlation for random pairs of
observations
sampleTuples Sample tuples of elements from a set
wpca Light-weight Weighted Principal Component
Analysis
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