Man pages for HenrikBengtsson/aroma.light-BioC_release
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
| 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 |
| findPeaksAndValleys | Finds extreme points in the empirical density estimated from... |
| 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... |
| likelihood.smooth.spline | Calculate the log likelihood of a smoothing spline given the... |
| medianPolish | Median polish |
| Non-documented_objects | Non-documented objects |
| 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... |
| normalizeQuantileRank.matrix | Normalizes the empirical distribution of a set of samples to... |
| normalizeQuantileSpline | Normalizes the empirical distribution of one or more samples... |
| normalizeTumorBoost | Normalizes allele B fractions for a tumor given a match... |
| pairedAlleleSpecificCopyNumbers | Calculating tumor-normal paired allele-specific copy number... |
| 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... |
| plotMvsMPairs | Plot log-ratios vs log-ratios for all pairs of columns |
| plotXYCurve | Plot the relationship between two variables as a smooth curve |
| print.SmoothSplineLikelihood | Prints an SmoothSplineLikelihood object |
| 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 |
