Files in metagenomeSeq

Statistical analysis for sparse high-throughput sequencing

README.md R/isItStillActive.R R/allClasses.R R/plotCorr.R R/cumNorm.R R/fitTimeSeries.R R/plotRare.R R/loadMeta.R R/MRexperiment2biom.R R/calculateEffectiveSamples.R R/misc.R R/cumNormMat.R R/fitLogNormal.R R/plotGenus.R R/doCountMStep.R R/doZeroMStep.R R/cumNormStat.R R/exportMat.R R/loadPhenoData.R R/plotFeature.R R/wrenchNorm.R R/plotOTU.R R/plotMRheatmap.R R/fitZeroLogNormal.R R/MRcoefs.R R/MRtable.R R/MRfulltable.R R/getEpsilon.R R/zigControl.R R/deprecated_metagenomeSeq_function.R R/plotOrd.R R/getNegativeLogLikelihoods.R R/plotBubble.R R/getPi.R R/fitPA.R R/biom2MRexperiment.R R/aggregateByTaxonomy.R R/aggregateBySample.R R/getCountDensity.R R/getZ.R R/doEStep.R R/MRihw.R R/filterData.R R/fitFeatureModel.R R/mergeMRexperiments.R R/fitDO.R R/fitZig.R R/loadBiom.R R/correlationTest.R R/loadMetaQ.R R/exportStats.R R/cumNormStatFast.R vignettes/overview.pdf man/plotTimeSeries.Rd man/getCountDensity.Rd man/metagenomeSeq-package.Rd man/loadMetaQ.Rd man/newMRexperiment.Rd man/extractMR.Rd man/plotGenus.Rd man/MRtable.Rd man/plotClassTimeSeries.Rd man/doZeroMStep.Rd man/cumNorm.Rd man/fitZig.Rd man/fitFeatureModel.Rd man/getPi.Rd man/fitZeroLogNormal.Rd man/aggregateBySample.Rd man/MRcoefs.Rd man/fitMultipleTimeSeries.Rd man/plotFeature.Rd man/makeLabels.Rd man/fitSSTimeSeries.Rd man/cumNormMat.Rd man/MRcounts.Rd man/metagenomeSeq-deprecated.Rd man/loadPhenoData.Rd man/posteriorProbs.Rd man/biom2MRexperiment.Rd man/normFactors.Rd man/MRihw-fitZigResults.Rd man/mergeMRexperiments.Rd man/loadMeta.Rd man/ts2MRexperiment.Rd man/calcNormFactors.Rd man/calcZeroAdjustment.Rd man/plotCorr.Rd man/trapz.Rd man/ssPerm.Rd man/correctIndices.Rd man/MRexperiment2biom.Rd man/plotBubble.Rd man/exportMat.Rd man/isItStillActive.Rd man/MRihw-fitFeatureModelResults.Rd man/mergeTable.Rd man/lungData.Rd man/expSummary.Rd man/loadBiom.Rd man/doCountMStep.Rd man/plotMRheatmap.Rd man/plotOrd.Rd man/fitZigResults-class.Rd man/fitTimeSeries.Rd man/fitPA.Rd man/zigControl.Rd man/fitLogNormal.Rd man/MRexperiment-class.Rd man/aggregateByTaxonomy.Rd man/plotOTU.Rd man/MRihw.Rd man/getZ.Rd man/wrenchNorm.Rd man/calcShrinkParameters.Rd man/mouseData.Rd man/calcStandardError.Rd man/normFactors-set.Rd man/cumNormStat.Rd man/plotRare.Rd man/uniqueFeatures.Rd man/cumNormStatFast.Rd man/calculateEffectiveSamples.Rd man/ssFit.Rd man/getEpsilon.Rd man/ssPermAnalysis.Rd man/fitDO.Rd man/filterData.Rd man/correlationTest.Rd man/libSize.Rd man/libSize-set.Rd man/ssIntervalCandidate.Rd man/getNegativeLogLikelihoods.Rd man/doEStep.Rd man/exportStats.Rd man/calcZeroComponent.Rd man/returnAppropriateObj.Rd man/calcPosComponent.Rd man/fitFeatureModelResults-class.Rd man/MRfulltable.Rd tests/testthat.R tests/testthat/test-norm.R tests/testthat/test-wrenchNorm.R tests/testthat/test-fitZig.R inst/doc/fitTimeSeries.R inst/doc/fitTimeSeries.pdf inst/doc/metagenomeSeq.pdf inst/doc/metagenomeSeq.R