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.

Author
Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Date of publication
None
Maintainer
Joseph N. Paulson <jpaulson@jimmy.harvard.edu>
License
Artistic-2.0
Version
1.16.0
URLs

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