Man pages for Bioconductor-mirror/metagenomeSeq
Statistical analysis for sparse high-throughput sequencing

aggregateBySampleAggregates a MRexperiment object or counts matrix to by a...
aggregateByTaxonomyAggregates a MRexperiment object or counts matrix to a...
biom2MRexperimentBiom to MRexperiment objects
calcNormFactorsCumulative sum scaling (css) normalization factors
calcPosComponentPositive component
calcShrinkParametersCalculate shrinkage parameters
calcStandardErrorCalculate the zero-inflated log-normal statistic's standard...
calculateEffectiveSamplesEstimated effective samples per feature
calcZeroAdjustmentCalculate the zero-inflated component's adjustment factor
calcZeroComponentZero component
correctIndicesCalculate the correct indices for the output of...
correlationTestCorrelation of each row of a matrix or MRexperiment object
cumNormCumulative sum scaling normalization
cumNormMatCumulative sum scaling factors.
cumNormStatCumulative sum scaling percentile selection
cumNormStatFastCumulative sum scaling percentile selection
doCountMStepCompute the Maximization step calculation for features still...
doEStepCompute the Expectation step.
doZeroMStepCompute the zero Maximization step.
exportMatExport the normalized MRexperiment dataset as a matrix.
exportStatsVarious statistics of the count data.
expSummaryAccess MRexperiment object experiment data
extractMRExtract the essentials of an MRexperiment.
filterDataFilter datasets according to no. features present in features...
fitDOWrapper to calculate Discovery Odds Ratios on feature values.
fitFeatureModelComputes differential abundance analysis using a...
fitLogNormalComputes a log-normal linear model and permutation based...
fitMultipleTimeSeriesDiscover differentially abundant time intervals for all...
fitPAWrapper to run fisher's test on presence/absence of a...
fitSSTimeSeriesDiscover differentially abundant time intervals using...
fitTimeSeriesDiscover differentially abundant time intervals
fitZeroLogNormalCompute the log fold-change estimates for the zero-inflated...
fitZigComputes the weighted fold-change estimates and t-statistics.
getCountDensityCompute the value of the count density function from the...
getEpsilonCalculate the relative difference between iterations of the...
getNegativeLogLikelihoodsCalculate the negative log-likelihoods for the various...
getPiCalculate the mixture proportions from the zero model / spike...
getZCalculate the current Z estimate responsibilities (posterior...
isItStillActiveFunction to determine if a feature is still active.
libSizeAccess sample depth of coverage from MRexperiment object
libSize-setReplace the library sizes in a MRexperiment object
loadBiomLoad objects organized in the Biom format.
loadMetaLoad a count dataset associated with a study.
loadMetaQLoad a count dataset associated with a study set up in a...
loadPhenoDataLoad a clinical/phenotypic dataset associated with a study.
lungDataOTU abundance matrix of samples from a smoker/non-smoker...
makeLabelsFunction to make labels simpler
mergeMRexperimentsMerge two MRexperiment objects together
mergeTableMerge two tables
metagenomeSeq-deprecatedDepcrecated functions in the metagenomeSeq package.
metagenomeSeq-packageStatistical analysis for sparse high-throughput sequencing
mouseDataOTU abundance matrix of mice samples from a diet longitudinal...
MRcoefsTable of top-ranked features from fitZig or fitFeatureModel
MRcountsAccessor for the counts slot of a MRexperiment object
MRexperiment2biomMRexperiment to biom objects
MRexperiment-classClass "MRexperiment" - a modified eSet object for the data...
MRfulltableTable of top microbial marker gene from linear model fit...
MRtableTable of top microbial marker gene from linear model fit...
newMRexperimentCreate a MRexperiment object
normFactorsAccess the normalization factors in a MRexperiment object
normFactors-setReplace the normalization factors in a MRexperiment object
plotBubbleBasic plot of binned vectors.
plotClassTimeSeriesPlot abundances by class
plotCorrBasic correlation plot function for normalized or...
plotFeatureBasic plot function of the raw or normalized data.
plotGenusBasic plot function of the raw or normalized data.
plotMRheatmapBasic heatmap plot function for normalized counts.
plotOrdPlot of either PCA or MDS coordinates for the distances of...
plotOTUBasic plot function of the raw or normalized data.
plotRarePlot of rarefaction effect
plotTimeSeriesPlot difference function for particular bacteria
posteriorProbsAccess the posterior probabilities that results from analysis
returnAppropriateObjCheck if MRexperiment or matrix and return matrix
ssFitsmoothing-splines anova fit
ssIntervalCandidatecalculate interesting time intervals
ssPermclass permutations for smoothing-spline time series analysis
ssPermAnalysissmoothing-splines anova fits for each permutation
trapzTrapezoidal Integration
ts2MRexperimentWith a list of fitTimeSeries results, generate an...
uniqueFeaturesTable of features unique to a group
zigControlSettings for the fitZig function
Bioconductor-mirror/metagenomeSeq documentation built on June 1, 2017, 11:49 a.m.