Files in microbiome/RPA

RPA: Robust Probabilistic Averaging for probe-level analysis

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

R/AllClasses.R R/AllGenerics.R R/RPA-package.R R/RPA.dcost.R R/RPA.iteration.R R/RPA.preprocess.R R/RPA.tau2.update.R R/calculate.rpa.hitchip.R R/d.update.fast.R R/estimate.affinities.R R/estimate.hyperparameters.R R/firstlib.R R/frpa.R R/get.probe.matrix.R R/get.probeset.hitchip.R R/initialize.priors.R R/internals.R R/levelmap.R R/n.phylotypes.per.oligo.R R/online.quantile.R R/plot-methods.R R/probe.performance.R R/retrieve.probesets.hitchip.R R/rpa.R R/rpa.complete.R R/rpa.fit.R R/rpa.online.R R/rpa.plot.R R/rpa.summarize.R R/show-methods.R R/summarize.batch.R R/summarize.batches.R R/summarize.rpa.hitchip.R R/summarize.sum.hitchip.R R/summarize_probedata_hitchip.R R/toydata.R R/update.hyperparameters.R R/updating.hyperparameters.R README.md

inst/CITATION

inst/NEWS

inst/extras/.gitignore

inst/extras/NAR2013/AffyComp/.gitignore

inst/extras/NAR2013/AffyComp/README

inst/extras/NAR2013/AffyComp/Table-test133.tab.gz.tex

inst/extras/NAR2013/AffyComp/Table-test133.tab.tex

inst/extras/NAR2013/AffyComp/Table-test95.tab.gz.tex

inst/extras/NAR2013/AffyComp/Table-test95.tab.tex

inst/extras/NAR2013/AffyComp/TableS1.tex.tex

inst/extras/NAR2013/AffyComp/affycomp-fRMA.R inst/extras/NAR2013/AffyComp/affycomp-fRPA.R inst/extras/NAR2013/AffyComp/affycomp.R inst/extras/NAR2013/AffyComp/comparison.tables.R inst/extras/NAR2013/AffyComp/get.hgu133atagpriors.R inst/extras/NAR2013/AffyComp/read.spikein.R

inst/extras/NAR2013/AffyComp/results-test133.tab.gz

inst/extras/NAR2013/AffyComp/results-test95.tab.gz

inst/extras/NAR2013/AffyComp/test.R inst/extras/NAR2013/AffyComp/test.affycomp.R

inst/extras/NAR2013/AffyComp/test133.tab.gz

inst/extras/NAR2013/AffyComp/test95.tab.gz

inst/extras/NAR2013/OnlineLearning/.gitignore

inst/extras/NAR2013/OnlineLearning/Classification-comparisons.Affymetrix2.tab

inst/extras/NAR2013/OnlineLearning/Classification-comparisons.Ensembl2.tab

inst/extras/NAR2013/OnlineLearning/EBI-Lukk-AltCDF-RPA.R inst/extras/NAR2013/OnlineLearning/Lukk-RPA-20120527.R inst/extras/NAR2013/OnlineLearning/Lukk-RPA-20120528.R inst/extras/NAR2013/OnlineLearning/Lukk-RPA-20121104.ENSG.R inst/extras/NAR2013/OnlineLearning/Lukk-RPA-20121104.R inst/extras/NAR2013/OnlineLearning/Lukk-RPA-20130216.R inst/extras/NAR2013/OnlineLearning/Lukk-RPA-ENSG-20120528.R inst/extras/NAR2013/OnlineLearning/Lukk-RPA-ENSG-20120606.R

inst/extras/NAR2013/OnlineLearning/README

inst/extras/NAR2013/OnlineLearning/SNPexampleforJ.R

inst/extras/NAR2013/OnlineLearning/TODO

inst/extras/NAR2013/OnlineLearning/altcdf-ENSEMBL.R inst/extras/NAR2013/OnlineLearning/altcdf-example.R inst/extras/NAR2013/OnlineLearning/altcdf.R inst/extras/NAR2013/OnlineLearning/batch.effects.R inst/extras/NAR2013/OnlineLearning/batch.size.effect.R inst/extras/NAR2013/OnlineLearning/ber.example.R inst/extras/NAR2013/OnlineLearning/check.R inst/extras/NAR2013/OnlineLearning/classification-comparison.R inst/extras/NAR2013/OnlineLearning/classification-plot.R inst/extras/NAR2013/OnlineLearning/classification-plot.tmp.R inst/extras/NAR2013/OnlineLearning/comparison.R inst/extras/NAR2013/OnlineLearning/debug.R inst/extras/NAR2013/OnlineLearning/example2.R inst/extras/NAR2013/OnlineLearning/init.R inst/extras/NAR2013/OnlineLearning/investigate.hyperparameters.R inst/extras/NAR2013/OnlineLearning/known.abatch.R inst/extras/NAR2013/OnlineLearning/loadData.R inst/extras/NAR2013/OnlineLearning/loadData2.R inst/extras/NAR2013/OnlineLearning/main-classification.R inst/extras/NAR2013/OnlineLearning/main.R inst/extras/NAR2013/OnlineLearning/main.test.R inst/extras/NAR2013/OnlineLearning/main2.R inst/extras/NAR2013/OnlineLearning/main2ENSG.R inst/extras/NAR2013/OnlineLearning/main2ENSGB.R inst/extras/NAR2013/OnlineLearning/misc.R inst/extras/NAR2013/OnlineLearning/online-tests.R inst/extras/NAR2013/OnlineLearning/online.test.R inst/extras/NAR2013/OnlineLearning/online.test2.R inst/extras/NAR2013/OnlineLearning/online.version.R inst/extras/NAR2013/OnlineLearning/parallel.R

inst/extras/NAR2013/OnlineLearning/probestd.evolution.example.probeset.jpg

inst/extras/NAR2013/OnlineLearning/rpa.online.debug.R inst/extras/NAR2013/OnlineLearning/runtimes-plot.R inst/extras/NAR2013/OnlineLearning/runtimetest.R inst/extras/NAR2013/OnlineLearning/sva.example.R inst/extras/NAR2013/OnlineLearning/test.R inst/extras/NAR2013/OnlineLearning/test.ebi.R inst/extras/NAR2013/OnlineLearning/test2.R inst/extras/NAR2013/OnlineLearning/test3.R inst/extras/NAR2013/OnlineLearning/testing.R inst/extras/NAR2013/OnlineLearning/validate.R inst/extras/NAR2013/OnlineLearning/validate.normalization.R inst/extras/NAR2013/fRPA/get.esets.R inst/extras/NAR2013/fRPA/main.R inst/extras/NAR2013/fRPA/main2.R inst/extras/NAR2013/fRPA/testing.R

inst/extras/bioc.txt

inst/extras/build.sh

inst/extras/document.R inst/extras/misc/compare.R inst/extras/misc/convert.vignette.R inst/extras/misc/examples/comparison.to.other.R inst/extras/misc/examples/example.R inst/extras/misc/examples/test.R inst/extras/misc/examples/testing.R inst/extras/misc/online.comparison1.R inst/extras/misc/online.comparison2.R inst/extras/misc/rpa.fit.test.R inst/extras/misc/sort.probes.R inst/extras/misc/tests/benchmark.R inst/extras/misc/tests/benchmark.rpa.R inst/extras/misc/tests/priortests.R inst/extras/misc/tests/rpa.fit.test.R man/RPA-package.Rd man/RPA.iteration.Rd man/RPA.preprocess.Rd man/calculate.rpa.Rd man/collect.hyperparameters.Rd man/d.update.fast.Rd man/estimate.affinities.Rd man/estimate.hyperparameters.Rd man/frpa.Rd man/get.batches.Rd man/get.probe.matrix.Rd man/get.probe.parameters.Rd man/get.probeset.Rd man/hyperparameter.update.Rd man/levelmap.Rd man/n.phylotypes.per.oligo.Rd man/online.quantile.Rd man/probe.parameters.tolist.Rd man/probe.performance.Rd man/probeplot.Rd man/probetable.Rd man/retrieve.probesets.Rd man/rpa.Rd man/rpa.complete.Rd man/rpa.fit.Rd man/rpa.online.Rd man/rpa.plot.Rd man/rpa.summarize.Rd man/rpaplot.Rd man/sample.probeset.Rd man/summarize.batch.Rd man/summarize.batches.Rd man/summarize.rpa.Rd man/summarize.sum.Rd man/summarize_probedata.Rd man/updating.hyperparameters.Rd tests/rpa.R vignettes/RPA.Rmd vignettes/RPA.md

microbiome/RPA documentation built on April 9, 2023, 10:59 a.m.