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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("metagenomeSeq")
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
Version1.16.0
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

Functions

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

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

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