metagenomeSeq: Statistical analysis for sparse high-throughput sequencing
Version 1.18.0

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
Bioconductor views Classification Clustering DifferentialExpression GeneticVariability Metagenomics Microbiome MultipleComparison Normalization Sequencing Software Visualization
Date of publicationNone
MaintainerJoseph N. Paulson <jpaulson@jimmy.harvard.edu>
LicenseArtistic-2.0
Version1.18.0
URL https://github.com/nosson/metagenomeSeq/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("metagenomeSeq")

Getting started

Package overview
README.md

Popular man pages

cumNorm: Cumulative sum scaling normalization
cumNormMat: Cumulative sum scaling factors.
fitFeatureModel: Computes differential abundance analysis using a...
loadMeta: Load a count dataset associated with a study.
MRtable: Table of top microbial marker gene from linear model fit...
newMRexperiment: Create a MRexperiment object
plotMRheatmap: Basic heatmap plot function for normalized counts.
See all...

All man pages Function index File listing

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

Functions

MRcoefs Man page Source code
MRcounts Man page Source code
MRcounts,MRexperiment-method Man page
MRexperiment-class Man page
MRexperiment2biom Man page Source code
MRfulltable Man page Source code
MRtable Man page Source code
[,MRexperiment,ANY,ANY,ANY-method Man page
[,MRexperiment-method Man page
aggSamp Man page Man page Source code
aggTax Man page Man page Source code
aggregateBySample Man page Source code
aggregateByTaxonomy Man page Source code
biom2MRexperiment Man page Source code
calcNormFactors Man page Source code
calcPosComponent Man page Source code
calcShrinkParameters Man page Source code
calcStandardError Man page Source code
calcZeroAdjustment Man page Source code
calcZeroComponent Man page Source code
calculateEffectiveSamples Man page Source code
colMeans,MRexperiment-method Man page
colSums,MRexperiment-method Man page
corTest Man page
correctIndices Man page Source code
correlationTest Man page Source code
cumNorm Man page Source code
cumNormMat Man page Source code
cumNormStat Man page Source code
cumNormStatFast Man page Source code
deprecated_metagenomeSeq_function Man page Source code
doCountMStep Man page Source code
doEStep Man page Source code
doZeroMStep Man page Source code
do_fitZig Source code
expSummary Man page Source code
expSummary,MRexperiment-method Man page
exportMat Man page Source code
exportMatrix Man page
exportStats Man page Source code
extractMR Man page Source code
filterData Man page Source code
fitDO Man page Source code
fitFeatureModel Man page Source code
fitLogNormal Man page Source code
fitMeta Man page Source code
fitMultipleTimeSeries Man page Source code
fitPA Man page Source code
fitSSTimeSeries Man page Source code
fitTimeSeries Man page Source code
fitZeroLogNormal Man page Source code
fitZig Man page Source code
genusPlot Man page
getCountDensity Man page Source code
getEpsilon Man page Source code
getNegativeLogLikelihoods Man page Source code
getPi Man page Source code
getZ Man page Source code
isItStillActive Man page Source code
libSize Man page
libSize,MRexperiment-method Man page
libSize<- Man page
libSize<-,MRexperiment,numeric-method Man page
loadBiom Man page Source code
loadMeta Man page Source code
loadMetaQ Man page Source code
loadPhenoData Man page Source code
load_biom Man page Source code
load_meta Man page Source code
load_metaQ Man page Source code
load_phenoData Man page Source code
lungData Man page
makeLabels Man page Source code
mergeMRexperiments Man page Source code
mergeTable Man page Source code
metadata Source code
metagenomeSeq Man page
metagenomeSeq-deprecated Man page
metagenomeSeq-deprecated-package Man page
metagenomeSeq-package Man page
metagenomicLoader Man page
mouseData Man page
newMRexperiment Man page Source code
normFactors Man page
normFactors,MRexperiment-method Man page
normFactors<- Man page
normFactors<-,MRexperiment,numeric-method Man page
phenoData Man page
plotBubble Man page Source code
plotClassTimeSeries Man page Source code
plotCorr Man page Source code
plotFeature Man page Source code
plotGenus Man page Source code
plotMRheatmap Man page Source code
plotOTU Man page Source code
plotOrd Man page Source code
plotRare Man page Source code
plotTimeSeries Man page Source code
posteriorProbs Man page Source code
posteriorProbs,MRexperiment-method Man page
qiimeLoader Man page
returnAppropriateObj Man page Source code
rowMeans,MRexperiment-method Man page
rowSums,MRexperiment-method Man page
settings2 Man page
ssFit Man page Source code
ssIntervalCandidate Man page Source code
ssPerm Man page Source code
ssPermAnalysis Man page Source code
trapz Man page Source code
ts2MRexperiment Man page Source code
uniqueFeatures Man page Source code
zigControl Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/MRcoefs.R
R/MRexperiment2biom.R
R/MRfulltable.R
R/MRtable.R
R/aggregateBySample.R
R/aggregateByTaxonomy.R
R/allClasses.R
R/biom2MRexperiment.R
R/calculateEffectiveSamples.R
R/correlationTest.R
R/cumNorm.R
R/cumNormMat.R
R/cumNormStat.R
R/cumNormStatFast.R
R/deprecated_metagenomeSeq_function.R
R/doCountMStep.R
R/doEStep.R
R/doZeroMStep.R
R/exportMat.R
R/exportStats.R
R/filterData.R
R/fitDO.R
R/fitFeatureModel.R
R/fitLogNormal.R
R/fitPA.R
R/fitTimeSeries.R
R/fitZeroLogNormal.R
R/fitZig.R
R/getCountDensity.R
R/getEpsilon.R
R/getNegativeLogLikelihoods.R
R/getPi.R
R/getZ.R
R/isItStillActive.R
R/loadBiom.R
R/loadMeta.R
R/loadMetaQ.R
R/loadPhenoData.R
R/mergeMRexperiments.R
R/misc.R
R/plotBubble.R
R/plotCorr.R
R/plotFeature.R
R/plotGenus.R
R/plotMRheatmap.R
R/plotOTU.R
R/plotOrd.R
R/plotRare.R
R/zigControl.R
README.md
build
build/vignette.rds
data
data/lungData.rda
data/mouseData.rda
inst
inst/CITATION
inst/doc
inst/doc/fitTimeSeries.R
inst/doc/fitTimeSeries.Rnw
inst/doc/fitTimeSeries.pdf
inst/doc/metagenomeSeq.R
inst/doc/metagenomeSeq.Rnw
inst/doc/metagenomeSeq.pdf
inst/extdata
inst/extdata/CHK_NAME.otus.count.csv
inst/extdata/CHK_clinical.csv
inst/extdata/CHK_otus.taxonomy.csv
inst/extdata/lungfit.rds
inst/unitTests
man
man/MRcoefs.Rd
man/MRcounts.Rd
man/MRexperiment-class.Rd
man/MRexperiment2biom.Rd
man/MRfulltable.Rd
man/MRtable.Rd
man/aggregateBySample.Rd
man/aggregateByTaxonomy.Rd
man/biom2MRexperiment.Rd
man/calcNormFactors.Rd
man/calcPosComponent.Rd
man/calcShrinkParameters.Rd
man/calcStandardError.Rd
man/calcZeroAdjustment.Rd
man/calcZeroComponent.Rd
man/calculateEffectiveSamples.Rd
man/correctIndices.Rd
man/correlationTest.Rd
man/cumNorm.Rd
man/cumNormMat.Rd
man/cumNormStat.Rd
man/cumNormStatFast.Rd
man/doCountMStep.Rd
man/doEStep.Rd
man/doZeroMStep.Rd
man/expSummary.Rd
man/exportMat.Rd
man/exportStats.Rd
man/extractMR.Rd
man/filterData.Rd
man/fitDO.Rd
man/fitFeatureModel.Rd
man/fitLogNormal.Rd
man/fitMultipleTimeSeries.Rd
man/fitPA.Rd
man/fitSSTimeSeries.Rd
man/fitTimeSeries.Rd
man/fitZeroLogNormal.Rd
man/fitZig.Rd
man/getCountDensity.Rd
man/getEpsilon.Rd
man/getNegativeLogLikelihoods.Rd
man/getPi.Rd
man/getZ.Rd
man/isItStillActive.Rd
man/libSize-set.Rd
man/libSize.Rd
man/loadBiom.Rd
man/loadMeta.Rd
man/loadMetaQ.Rd
man/loadPhenoData.Rd
man/lungData.Rd
man/makeLabels.Rd
man/mergeMRexperiments.Rd
man/mergeTable.Rd
man/metagenomeSeq-deprecated.Rd
man/metagenomeSeq-package.Rd
man/mouseData.Rd
man/newMRexperiment.Rd
man/normFactors-set.Rd
man/normFactors.Rd
man/plotBubble.Rd
man/plotClassTimeSeries.Rd
man/plotCorr.Rd
man/plotFeature.Rd
man/plotGenus.Rd
man/plotMRheatmap.Rd
man/plotOTU.Rd
man/plotOrd.Rd
man/plotRare.Rd
man/plotTimeSeries.Rd
man/posteriorProbs.Rd
man/returnAppropriateObj.Rd
man/ssFit.Rd
man/ssIntervalCandidate.Rd
man/ssPerm.Rd
man/ssPermAnalysis.Rd
man/trapz.Rd
man/ts2MRexperiment.Rd
man/uniqueFeatures.Rd
man/zigControl.Rd
tests
tests/test_datasets
tests/testthat
tests/testthat.R
tests/testthat/test-fitZig.R
tests/testthat/test-norm.R
vignettes
vignettes/fitTimeSeries.Rnw
vignettes/fitTimeSeries.bib
vignettes/metagenomeSeq.Rnw
vignettes/metagenomeSeq.bib
vignettes/metagenomeSeq_figure1.png
vignettes/metagenomeSeq_figure2.png
vignettes/overview.pdf
metagenomeSeq documentation built on May 20, 2017, 9:57 p.m.

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