MRcoefs                 Table of top-ranked features from fitZig or
                        fitFeatureModel
MRcounts                Accessor for the counts slot of a MRexperiment
                        object
MRexperiment-class      Class "MRexperiment" - a modified eSet object
                        for the data from high-throughput sequencing
                        experiments
MRexperiment2biom       MRexperiment to biom objects
MRfulltable             Table of top microbial marker gene from linear
                        model fit including sequence information
MRtable                 Table of top microbial marker gene from linear
                        model fit including sequence information
aggregateBySample       Aggregates a MRexperiment object or counts
                        matrix to by a factor.
aggregateByTaxonomy     Aggregates a MRexperiment object or counts
                        matrix to a particular level.
biom2MRexperiment       Biom to MRexperiment objects
calcNormFactors         Cumulative sum scaling (css) normalization
                        factors
calcPosComponent        Positive component
calcShrinkParameters    Calculate shrinkage parameters
calcStandardError       Calculate the zero-inflated log-normal
                        statistic's standard error
calcZeroAdjustment      Calculate the zero-inflated component's
                        adjustment factor
calcZeroComponent       Zero component
calculateEffectiveSamples
                        Estimated effective samples per feature
correctIndices          Calculate the correct indices for the output of
                        correlationTest
correlationTest         Correlation of each row of a matrix or
                        MRexperiment object
cumNorm                 Cumulative sum scaling normalization
cumNormMat              Cumulative sum scaling factors.
cumNormStat             Cumulative sum scaling percentile selection
cumNormStatFast         Cumulative sum scaling percentile selection
doCountMStep            Compute the Maximization step calculation for
                        features still active.
doEStep                 Compute the Expectation step.
doZeroMStep             Compute the zero Maximization step.
expSummary              Access MRexperiment object experiment data
exportMat               Export the normalized MRexperiment dataset as a
                        matrix.
exportStats             Various statistics of the count data.
extractMR               Extract the essentials of an MRexperiment.
filterData              Filter datasets according to no. features
                        present in features with at least a certain
                        depth.
fitDO                   Wrapper to calculate Discovery Odds Ratios on
                        feature values.
fitFeatureModel         Computes differential abundance analysis using
                        a zero-inflated log-normal model
fitLogNormal            Computes a log-normal linear model and
                        permutation based p-values.
fitMultipleTimeSeries   Discover differentially abundant time intervals
                        for all bacteria
fitPA                   Wrapper to run fisher's test on
                        presence/absence of a feature.
fitSSTimeSeries         Discover differentially abundant time intervals
                        using SS-Anova
fitTimeSeries           Discover differentially abundant time intervals
fitZeroLogNormal        Compute the log fold-change estimates for the
                        zero-inflated log-normal model
fitZig                  Computes the weighted fold-change estimates and
                        t-statistics.
getCountDensity         Compute the value of the count density function
                        from the count model residuals.
getEpsilon              Calculate the relative difference between
                        iterations of the negative log-likelihoods.
getNegativeLogLikelihoods
                        Calculate the negative log-likelihoods for the
                        various features given the residuals.
getPi                   Calculate the mixture proportions from the zero
                        model / spike mass model residuals.
getZ                    Calculate the current Z estimate
                        responsibilities (posterior probabilities)
isItStillActive         Function to determine if a feature is still
                        active.
libSize                 Access sample depth of coverage from
                        MRexperiment object
libSize<-               Replace the library sizes in a MRexperiment
                        object
loadBiom                Load objects organized in the Biom format.
loadMeta                Load a count dataset associated with a study.
loadMetaQ               Load a count dataset associated with a study
                        set up in a Qiime format.
loadPhenoData           Load a clinical/phenotypic dataset associated
                        with a study.
lungData                OTU abundance matrix of samples from a
                        smoker/non-smoker study
makeLabels              Function to make labels simpler
mergeMRexperiments      Merge two MRexperiment objects together
mergeTable              Merge two tables
metagenomeSeq-deprecated
                        Depcrecated functions in the metagenomeSeq
                        package.
metagenomeSeq-package   Statistical analysis for sparse high-throughput
                        sequencing
mouseData               OTU abundance matrix of mice samples from a
                        diet longitudinal study
newMRexperiment         Create a MRexperiment object
normFactors             Access the normalization factors in a
                        MRexperiment object
normFactors<-           Replace the normalization factors in a
                        MRexperiment object
plotBubble              Basic plot of binned vectors.
plotClassTimeSeries     Plot abundances by class
plotCorr                Basic correlation plot function for normalized
                        or unnormalized counts.
plotFeature             Basic plot function of the raw or normalized
                        data.
plotGenus               Basic plot function of the raw or normalized
                        data.
plotMRheatmap           Basic heatmap plot function for normalized
                        counts.
plotOTU                 Basic plot function of the raw or normalized
                        data.
plotOrd                 Plot of either PCA or MDS coordinates for the
                        distances of normalized or unnormalized counts.
plotRare                Plot of rarefaction effect
plotTimeSeries          Plot difference function for particular
                        bacteria
posteriorProbs          Access the posterior probabilities that results
                        from analysis
returnAppropriateObj    Check if MRexperiment or matrix and return
                        matrix
ssFit                   smoothing-splines anova fit
ssIntervalCandidate     calculate interesting time intervals
ssPerm                  class permutations for smoothing-spline time
                        series analysis
ssPermAnalysis          smoothing-splines anova fits for each
                        permutation
trapz                   Trapezoidal Integration
ts2MRexperiment         With a list of fitTimeSeries results, generate
                        an MRexperiment that can be plotted with
                        metavizr
uniqueFeatures          Table of features unique to a group
zigControl              Settings for the fitZig function
