Package 'metagenomeSeq' - Bioconductor

Index∗Topic packagemetagenomeSeq-package, 3[,MRexperiment-method (MRexperiment), 30aggregateByTaxonomy, 3aggTax (aggregateByTaxonomy), 3biom2MRexperiment, 4, 24, 31calculateEffectiveSamples, 5colMeans,MRexperiment-method(MRexperiment), 30colSums,MRexperiment-method(MRexperiment), 30correctIndices, 6correlationTest, 6corTest (correlationTest), 6cumNorm, 7, 8–10, 13, 14, 16, 18, 19, 30, 37,38, 41, 44cumNormMat, 8, 30, 36, 39, 40cumNormStat, 8, 9, 10, 30cumNormStatFast, 9, 10doCountMStep, 10doEStep, 11doZeroMStep, 12exportMat, 13exportMatrix (exportMat), 13exportStats, 14expSummary, 14expSummary,MRexperiment-method(expSummary), 14filterData, 15fitDO, 16fitMeta, 17fitPA, 17, 33fitZig, 5, 8–13, 16, 18, 18–23, 28, 33, 34, 43,44genusPlot (plotGenus), 38getCountDensity, 19getEpsilon, 20getNegativeLogLikelihoods, 20getPi, 21getZ, 22isItStillActive, 22libSize, 23, 30libSize,MRexperiment-method (libSize),23load_biom, 5, 24, 31load_meta, 5, 24, 24–26, 31load_metaQ, 25load_phenoData, 5, 24, 25, 26, 31lungData, 26makeLabels, 27metagenomeSeq (metagenomeSeq-package), 3metagenomeSeq-package, 3metagenomicLoader (load_meta), 24mouseData, 27MRcoefs, 5, 28, 33, 34MRcounts, 29, 30MRcounts,MRexperiment-method(MRcounts), 29MRexperiment, 30MRexperiment-class (MRexperiment), 30MRexperiment2biom, 31MRfulltable, 5, 32MRtable, 28, 33, 33newMRexperiment, 5, 24, 30, 31, 34normFactors, 30, 35normFactors,MRexperiment-method(normFactors), 35p.adjust, 28, 32, 33phenoData (load_phenoData), 26plotCorr, 36, 4245