RPA: Robust Probabilistic Averaging for probe-level analysis


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Documentation for package ‘RPA’ version 1.22.0

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RPA-package RPA: probabilistic analysis of probe reliability and gene expression
collect.hyperparameters collect.hyperparameters
d.update.fast d.update.fast
estimate.affinities estimate.affinities
estimate.hyperparameters estimate.hyperparameters Hyperparameter estimation
frpa frpa frozen-RPA preprocessing using precalculated probe parameters
get.batches get.batches Split data into batches
get.probe.matrix get.probe.matrix
get.probe.parameters get.probe.parameters
hyperparameter.update hyperparameter.update Update hyperparameters Update shape (alpha) and scale (beta) parameters of the inverse gamma distribution.
online.quantile online.quantile Quantile normalization tools for online preprocessing. Estimate quantiles for quantile normalization based on subset of the data (random, or specified by the user).
probe.parameters.tolist probe.parameters.tolist
probe.performance probe.performance
probeplot probeplot Plot RPA results and probe-level data for a specified probeset.
probetable probetable
RPA RPA: probabilistic analysis of probe reliability and gene expression
rpa rpa Wrapper for RPA preprocessing.
rpa.complete rpa.complete RPA preprocessing, also returns probe parameters
rpa.fit rpa.fit
RPA.iteration RPA.iteration Estimating model parameters d and tau2.
rpa.online rpa.online RPA-online for preprocessing very large expression data sets.
rpa.plot rpa.plot Plot RPA results and probe-level data for a specified probeset.
RPA.preprocess RPA.preprocess Preprocess AffyBatch object for RPA.
rpa.summarize rpa.summarize
rpaplot rpaplot Plot RPA results and probe-level data for a specified probeset.
sample.probeset sample.probeset Toydata generator for probeset data.
summarize.batch summarize.batch
summarize.batches summarize.batches
updating.hyperparameters updating.hyperparameters Hyperparameter update