metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.

AuthorJoseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Date of publicationNone
MaintainerJoseph N. Paulson <jpaulson@jimmy.harvard.edu>
LicenseArtistic-2.0
Version1.16.0
https://github.com/nosson/metagenomeSeq/

View on Bioconductor

Man pages

aggregateBySample: Aggregates a MRexperiment object or counts matrix to by a...

aggregateByTaxonomy: Aggregates a MRexperiment object or counts matrix to a...

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...

calculateEffectiveSamples: Estimated effective samples per feature

calcZeroAdjustment: Calculate the zero-inflated component's adjustment factor

calcZeroComponent: Zero component

correctIndices: Calculate the correct indices for the output of...

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...

doEStep: Compute the Expectation step.

doZeroMStep: Compute the zero Maximization step.

exportMat: Export the normalized MRexperiment dataset as a matrix.

exportStats: Various statistics of the count data.

expSummary: Access MRexperiment object experiment data

extractMR: Extract the essentials of an MRexperiment.

filterData: Filter datasets according to no. features present in features...

fitDO: Wrapper to calculate Discovery Odds Ratios on feature values.

fitFeatureModel: Computes differential abundance analysis using a...

fitLogNormal: Computes a log-normal linear model and permutation based...

fitMultipleTimeSeries: Discover differentially abundant time intervals for all...

fitPA: Wrapper to run fisher's test on presence/absence of a...

fitSSTimeSeries: Discover differentially abundant time intervals using...

fitTimeSeries: Discover differentially abundant time intervals

fitZeroLogNormal: Compute the log fold-change estimates for the zero-inflated...

fitZig: Computes the weighted fold-change estimates and t-statistics.

getCountDensity: Compute the value of the count density function from the...

getEpsilon: Calculate the relative difference between iterations of the...

getNegativeLogLikelihoods: Calculate the negative log-likelihoods for the various...

getPi: Calculate the mixture proportions from the zero model / spike...

getZ: Calculate the current Z estimate responsibilities (posterior...

isItStillActive: Function to determine if a feature is still active.

libSize: Access sample depth of coverage from MRexperiment object

libSize-set: 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...

loadPhenoData: Load a clinical/phenotypic dataset associated with a study.

lungData: OTU abundance matrix of samples from a smoker/non-smoker...

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...

MRcoefs: Table of top-ranked features from fitZig or fitFeatureModel

MRcounts: Accessor for the counts slot of a MRexperiment object

MRexperiment2biom: MRexperiment to biom objects

MRexperiment-class: Class "MRexperiment" - a modified eSet object for the data...

MRfulltable: Table of top microbial marker gene from linear model fit...

MRtable: Table of top microbial marker gene from linear model fit...

newMRexperiment: Create a MRexperiment object

normFactors: Access the normalization factors in a MRexperiment object

normFactors-set: 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...

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.

plotOrd: Plot of either PCA or MDS coordinates for the distances of...

plotOTU: Basic plot function of the raw or normalized data.

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...

uniqueFeatures: Table of features unique to a group

zigControl: Settings for the fitZig function

Files in this package

metagenomeSeq/DESCRIPTION
metagenomeSeq/NAMESPACE
metagenomeSeq/NEWS
metagenomeSeq/R
metagenomeSeq/R/MRcoefs.R metagenomeSeq/R/MRexperiment2biom.R metagenomeSeq/R/MRfulltable.R metagenomeSeq/R/MRtable.R metagenomeSeq/R/aggregateBySample.R metagenomeSeq/R/aggregateByTaxonomy.R metagenomeSeq/R/allClasses.R metagenomeSeq/R/biom2MRexperiment.R metagenomeSeq/R/calculateEffectiveSamples.R metagenomeSeq/R/correlationTest.R metagenomeSeq/R/cumNorm.R metagenomeSeq/R/cumNormMat.R metagenomeSeq/R/cumNormStat.R metagenomeSeq/R/cumNormStatFast.R metagenomeSeq/R/deprecated_metagenomeSeq_function.R metagenomeSeq/R/doCountMStep.R metagenomeSeq/R/doEStep.R metagenomeSeq/R/doZeroMStep.R metagenomeSeq/R/exportMat.R metagenomeSeq/R/exportStats.R metagenomeSeq/R/filterData.R metagenomeSeq/R/fitDO.R metagenomeSeq/R/fitFeatureModel.R metagenomeSeq/R/fitLogNormal.R metagenomeSeq/R/fitPA.R metagenomeSeq/R/fitTimeSeries.R metagenomeSeq/R/fitZeroLogNormal.R metagenomeSeq/R/fitZig.R metagenomeSeq/R/getCountDensity.R metagenomeSeq/R/getEpsilon.R metagenomeSeq/R/getNegativeLogLikelihoods.R metagenomeSeq/R/getPi.R metagenomeSeq/R/getZ.R metagenomeSeq/R/isItStillActive.R metagenomeSeq/R/loadBiom.R metagenomeSeq/R/loadMeta.R metagenomeSeq/R/loadMetaQ.R metagenomeSeq/R/loadPhenoData.R metagenomeSeq/R/mergeMRexperiments.R metagenomeSeq/R/misc.R metagenomeSeq/R/plotBubble.R metagenomeSeq/R/plotCorr.R metagenomeSeq/R/plotFeature.R metagenomeSeq/R/plotGenus.R metagenomeSeq/R/plotMRheatmap.R metagenomeSeq/R/plotOTU.R metagenomeSeq/R/plotOrd.R metagenomeSeq/R/plotRare.R metagenomeSeq/R/zigControl.R
metagenomeSeq/README.md
metagenomeSeq/build
metagenomeSeq/build/vignette.rds
metagenomeSeq/data
metagenomeSeq/data/lungData.rda
metagenomeSeq/data/mouseData.rda
metagenomeSeq/inst
metagenomeSeq/inst/CITATION
metagenomeSeq/inst/doc
metagenomeSeq/inst/doc/fitTimeSeries.R
metagenomeSeq/inst/doc/fitTimeSeries.Rnw
metagenomeSeq/inst/doc/fitTimeSeries.pdf
metagenomeSeq/inst/doc/metagenomeSeq.R
metagenomeSeq/inst/doc/metagenomeSeq.Rnw
metagenomeSeq/inst/doc/metagenomeSeq.pdf
metagenomeSeq/inst/extdata
metagenomeSeq/inst/extdata/CHK_NAME.otus.count.csv
metagenomeSeq/inst/extdata/CHK_clinical.csv
metagenomeSeq/inst/extdata/CHK_otus.taxonomy.csv
metagenomeSeq/inst/extdata/lungfit.rds
metagenomeSeq/inst/unitTests
metagenomeSeq/man
metagenomeSeq/man/MRcoefs.Rd metagenomeSeq/man/MRcounts.Rd metagenomeSeq/man/MRexperiment-class.Rd metagenomeSeq/man/MRexperiment2biom.Rd metagenomeSeq/man/MRfulltable.Rd metagenomeSeq/man/MRtable.Rd metagenomeSeq/man/aggregateBySample.Rd metagenomeSeq/man/aggregateByTaxonomy.Rd metagenomeSeq/man/biom2MRexperiment.Rd metagenomeSeq/man/calcNormFactors.Rd metagenomeSeq/man/calcPosComponent.Rd metagenomeSeq/man/calcShrinkParameters.Rd metagenomeSeq/man/calcStandardError.Rd metagenomeSeq/man/calcZeroAdjustment.Rd metagenomeSeq/man/calcZeroComponent.Rd metagenomeSeq/man/calculateEffectiveSamples.Rd metagenomeSeq/man/correctIndices.Rd metagenomeSeq/man/correlationTest.Rd metagenomeSeq/man/cumNorm.Rd metagenomeSeq/man/cumNormMat.Rd metagenomeSeq/man/cumNormStat.Rd metagenomeSeq/man/cumNormStatFast.Rd metagenomeSeq/man/doCountMStep.Rd metagenomeSeq/man/doEStep.Rd metagenomeSeq/man/doZeroMStep.Rd metagenomeSeq/man/expSummary.Rd metagenomeSeq/man/exportMat.Rd metagenomeSeq/man/exportStats.Rd metagenomeSeq/man/extractMR.Rd metagenomeSeq/man/filterData.Rd metagenomeSeq/man/fitDO.Rd metagenomeSeq/man/fitFeatureModel.Rd metagenomeSeq/man/fitLogNormal.Rd metagenomeSeq/man/fitMultipleTimeSeries.Rd metagenomeSeq/man/fitPA.Rd metagenomeSeq/man/fitSSTimeSeries.Rd metagenomeSeq/man/fitTimeSeries.Rd metagenomeSeq/man/fitZeroLogNormal.Rd metagenomeSeq/man/fitZig.Rd metagenomeSeq/man/getCountDensity.Rd metagenomeSeq/man/getEpsilon.Rd metagenomeSeq/man/getNegativeLogLikelihoods.Rd metagenomeSeq/man/getPi.Rd metagenomeSeq/man/getZ.Rd metagenomeSeq/man/isItStillActive.Rd metagenomeSeq/man/libSize-set.Rd metagenomeSeq/man/libSize.Rd metagenomeSeq/man/loadBiom.Rd metagenomeSeq/man/loadMeta.Rd metagenomeSeq/man/loadMetaQ.Rd metagenomeSeq/man/loadPhenoData.Rd metagenomeSeq/man/lungData.Rd metagenomeSeq/man/makeLabels.Rd metagenomeSeq/man/mergeMRexperiments.Rd metagenomeSeq/man/mergeTable.Rd metagenomeSeq/man/metagenomeSeq-deprecated.Rd metagenomeSeq/man/metagenomeSeq-package.Rd metagenomeSeq/man/mouseData.Rd metagenomeSeq/man/newMRexperiment.Rd metagenomeSeq/man/normFactors-set.Rd metagenomeSeq/man/normFactors.Rd metagenomeSeq/man/plotBubble.Rd metagenomeSeq/man/plotClassTimeSeries.Rd metagenomeSeq/man/plotCorr.Rd metagenomeSeq/man/plotFeature.Rd metagenomeSeq/man/plotGenus.Rd metagenomeSeq/man/plotMRheatmap.Rd metagenomeSeq/man/plotOTU.Rd metagenomeSeq/man/plotOrd.Rd metagenomeSeq/man/plotRare.Rd metagenomeSeq/man/plotTimeSeries.Rd metagenomeSeq/man/posteriorProbs.Rd metagenomeSeq/man/returnAppropriateObj.Rd metagenomeSeq/man/ssFit.Rd metagenomeSeq/man/ssIntervalCandidate.Rd metagenomeSeq/man/ssPerm.Rd metagenomeSeq/man/ssPermAnalysis.Rd metagenomeSeq/man/trapz.Rd metagenomeSeq/man/ts2MRexperiment.Rd metagenomeSeq/man/uniqueFeatures.Rd metagenomeSeq/man/zigControl.Rd
metagenomeSeq/tests
metagenomeSeq/tests/test_datasets
metagenomeSeq/tests/testthat
metagenomeSeq/tests/testthat.R
metagenomeSeq/tests/testthat/test-fitZig.R
metagenomeSeq/tests/testthat/test-norm.R
metagenomeSeq/vignettes
metagenomeSeq/vignettes/fitTimeSeries.Rnw
metagenomeSeq/vignettes/fitTimeSeries.bib
metagenomeSeq/vignettes/metagenomeSeq.Rnw
metagenomeSeq/vignettes/metagenomeSeq.bib
metagenomeSeq/vignettes/metagenomeSeq_figure1.png
metagenomeSeq/vignettes/metagenomeSeq_figure2.png
metagenomeSeq/vignettes/overview.pdf

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