| Statistical analysis for sparse high-throughput sequencing | metagenomeSeq-package metagenomeSeq |
| Aggregates a MRexperiment object or counts matrix to by a factor. | aggregateBySample aggSamp |
| Aggregates a MRexperiment object or counts matrix to a particular level. | aggregateByTaxonomy aggTax |
| Biom to MRexperiment objects | biom2MRexperiment |
| Cumulative sum scaling (css) normalization factors | calcNormFactors |
| Positive component | calcPosComponent |
| Calculate shrinkage parameters | calcShrinkParameters |
| Calculate the zero-inflated log-normal statistic's standard error | calcStandardError |
| Estimated effective samples per feature | calculateEffectiveSamples |
| Calculate the zero-inflated component's adjustment factor | calcZeroAdjustment |
| Zero component | calcZeroComponent |
| Calculate the correct indices for the output of correlationTest | correctIndices |
| Correlation of each row of a matrix or MRexperiment object | correlationTest corTest |
| Cumulative sum scaling normalization | cumNorm |
| Cumulative sum scaling factors. | cumNormMat |
| Cumulative sum scaling percentile selection | cumNormStat |
| Cumulative sum scaling percentile selection | cumNormStatFast |
| Compute the Maximization step calculation for features still active. | doCountMStep |
| Compute the Expectation step. | doEStep |
| Compute the zero Maximization step. | doZeroMStep |
| Export the normalized MRexperiment dataset as a matrix. | exportMat exportMatrix |
| Various statistics of the count data. | exportStats |
| Access MRexperiment object experiment data | expSummary expSummary,MRexperiment-method |
| Extract the essentials of an MRexperiment. | extractMR |
| Filter datasets according to no. features present in features with at least a certain depth. | filterData |
| Wrapper to calculate Discovery Odds Ratios on feature values. | fitDO |
| Computes differential abundance analysis using a zero-inflated log-normal model | fitFeatureModel |
| Class "fitFeatureModelResults" - a formal class for storing results from a fitFeatureModel call | fitFeatureModelResults-class |
| Computes a log-normal linear model and permutation based p-values. | fitLogNormal |
| Discover differentially abundant time intervals for all bacteria | fitMultipleTimeSeries |
| Wrapper to run fisher's test on presence/absence of a feature. | fitPA |
| Discover differentially abundant time intervals using SS-Anova | fitSSTimeSeries |
| Discover differentially abundant time intervals | fitTimeSeries |
| Compute the log fold-change estimates for the zero-inflated log-normal model | fitZeroLogNormal |
| Computes the weighted fold-change estimates and t-statistics. | fitZig |
| Class "fitZigResults" - a formal class for storing results from a fitZig call | fitZigResults-class |
| Compute the value of the count density function from the count model residuals. | getCountDensity |
| Calculate the relative difference between iterations of the negative log-likelihoods. | getEpsilon |
| Calculate the negative log-likelihoods for the various features given the residuals. | getNegativeLogLikelihoods |
| Calculate the mixture proportions from the zero model / spike mass model residuals. | getPi |
| Calculate the current Z estimate responsibilities (posterior probabilities) | getZ |
| Function to determine if a feature is still active. | isItStillActive |
| Access sample depth of coverage from MRexperiment object | libSize |
| Replace the library sizes in a MRexperiment object | libSize<- libSize<-,MRexperiment,numeric-method |
| Load objects organized in the Biom format. | loadBiom |
| Load a count dataset associated with a study. | loadMeta metagenomicLoader |
| Load a count dataset associated with a study set up in a Qiime format. | loadMetaQ qiimeLoader |
| Load a clinical/phenotypic dataset associated with a study. | loadPhenoData phenoData |
| OTU abundance matrix of samples from a smoker/non-smoker study | lungData |
| Function to make labels simpler | makeLabels |
| Merge two MRexperiment objects together | mergeMRexperiments |
| Merge two tables | mergeTable |
| Depcrecated functions in the metagenomeSeq package. | deprecated_metagenomeSeq_function fitMeta load_biom load_meta load_metaQ load_phenoData metagenomeSeq-deprecated |
| OTU abundance matrix of mice samples from a diet longitudinal study | mouseData |
| Table of top-ranked features from fitZig or fitFeatureModel | MRcoefs |
| Accessor for the counts slot of a MRexperiment object | MRcounts MRcounts,MRexperiment-method |
| Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments | colMeans,MRexperiment-method colSums,MRexperiment-method libSize,MRexperiment-method MRexperiment-class normFactors,MRexperiment-method rowMeans,MRexperiment-method rowSums,MRexperiment-method [,MRexperiment,ANY,ANY,ANY-method [,MRexperiment-method |
| MRexperiment to biom objects | MRexperiment2biom |
| Table of top microbial marker gene from linear model fit including sequence information | MRfulltable |
| MRihw runs IHW within a MRcoefs() call | MRihw |
| MRihw runs IHW within a MRcoefs() call | MRihw,fitFeatureModelResults-method |
| MRihw runs IHW within a MRcoefs() call | MRihw,fitZigResults-method |
| Table of top microbial marker gene from linear model fit including sequence information | MRtable |
| Create a MRexperiment object | newMRexperiment |
| Access the normalization factors in a MRexperiment object | normFactors |
| Replace the normalization factors in a MRexperiment object | normFactors<- normFactors<-,MRexperiment,numeric-method |
| Basic plot of binned vectors. | plotBubble |
| Plot abundances by class | plotClassTimeSeries |
| Basic correlation plot function for normalized or unnormalized counts. | plotCorr |
| Basic plot function of the raw or normalized data. | plotFeature |
| Basic plot function of the raw or normalized data. | genusPlot plotGenus |
| Basic heatmap plot function for normalized counts. | plotMRheatmap |
| Plot of either PCA or MDS coordinates for the distances of normalized or unnormalized counts. | plotOrd |
| Basic plot function of the raw or normalized data. | plotOTU |
| Plot of rarefaction effect | plotRare |
| Plot difference function for particular bacteria | plotTimeSeries |
| Access the posterior probabilities that results from analysis | posteriorProbs posteriorProbs,MRexperiment-method |
| Check if MRexperiment or matrix and return matrix | returnAppropriateObj |
| smoothing-splines anova fit | ssFit |
| calculate interesting time intervals | ssIntervalCandidate |
| class permutations for smoothing-spline time series analysis | ssPerm |
| smoothing-splines anova fits for each permutation | ssPermAnalysis |
| Trapezoidal Integration | trapz |
| With a list of fitTimeSeries results, generate an MRexperiment that can be plotted with metavizr | ts2MRexperiment |
| Table of features unique to a group | uniqueFeatures |
| Computes normalization factors using wrench instead of cumNorm | wrenchNorm |
| Settings for the fitZig function | settings2 zigControl |
