Statistical analysis for sparse high-throughput sequencing


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Documentation for package ‘metagenomeSeq’ version 1.12.1

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metagenomeSeq-deprecated-package Depcrecated functions in the metagenomeSeq package.
metagenomeSeq-package Statistical analysis for sparse high-throughput sequencing
aggregateBySample Aggregates a MRexperiment object or counts matrix to by a factor.
aggregateByTaxonomy Aggregates a MRexperiment object or counts matrix to a particular level.
aggSamp Aggregates a MRexperiment object or counts matrix to by a factor.
aggTax Aggregates a MRexperiment object or counts matrix to a particular level.
biom2MRexperiment Biome to MRexperiment objects
calcNormFactors Cumulative sum scaling normalization factors Return a vector of the the sum up to and including a quantile.
calcPosComponent Positive component
calcShrinkParameters Calculate shrinkage parameters
calcStandardError Calculate the zero-inflated log-normal statistic's standard error
calculateEffectiveSamples Estimated effective samples per feature
calcZeroAdjustment Calculate the zero-inflated component's adjustment factor
calcZeroComponent Zero component
colMeans-method Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments
colSums-method Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments
correctIndices Calculate the correct indices for the output of correlationTest
correlationTest Correlation of each row of a matrix or MRexperiment object
corTest 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
deprecated_metagenomeSeq_function Depcrecated functions in the metagenomeSeq package.
doCountMStep Compute the Maximization step calculation for features still active.
doEStep Compute the Expectation step.
doZeroMStep Compute the zero Maximization step.
exportMat Export the normalized MRexperiment dataset as a matrix.
exportMatrix Export the normalized MRexperiment dataset as a matrix.
exportStats Various statistics of the count data.
expSummary Access MRexperiment object experiment data
expSummary-method Access MRexperiment object experiment data
filterData Filter datasets according to no. features present in features with at least a certain depth.
fitDO Wrapper to calculate Discovery Odds Ratios on feature values.
fitFeatureModel Computes differential abundance analysis using a zero-inflated log-normal model
fitLogNormal Computes a log-normal linear model and permutation based p-values.
fitMeta Depcrecated functions in the metagenomeSeq package.
fitPA Wrapper to run fisher's test on presence/absence of a feature.
fitSSTimeSeries Discover differentially abundant time intervals using SS-Anova
fitTimeSeries Discover differentially abundant time intervals
fitZeroLogNormal Compute the log fold-change estimates for the zero-inflated log-normal model
fitZig Computes the weighted fold-change estimates and t-statistics.
genusPlot Basic plot function of the raw or normalized data.
getCountDensity Compute the value of the count density function from the count model residuals.
getEpsilon Calculate the relative difference between iterations of the negative log-likelihoods.
getNegativeLogLikelihoods Calculate the negative log-likelihoods for the various features given the residuals.
getPi Calculate the mixture proportions from the zero model / spike mass model residuals.
getZ Calculate the current Z estimate responsibilities (posterior probabilities)
isItStillActive Function to determine if a feature is still active.
libSize Access sample depth of coverage from MRexperiment object
libSize-method Access sample depth of coverage from MRexperiment object
load_biom Load objects organized in the Biome format.
load_meta Load a count dataset associated with a study.
load_metaQ Load a count dataset associated with a study set up in a Qiime format.
load_phenoData Load a clinical/phenotypic dataset associated with a study.
lungData OTU abundance matrix of samples from a smoker/non-smoker study
makeLabels Function to make labels simpler
metagenomeSeq Statistical analysis for sparse high-throughput sequencing
metagenomeSeq-deprecated Depcrecated functions in the metagenomeSeq package.
metagenomicLoader Load a count dataset associated with a study.
mouseData OTU abundance matrix of mice samples from a diet longitudinal study
MRcoefs Table of top-ranked features from fitZig or fitFeatureModel
MRcounts Accessor for the counts slot of a MRexperiment object
MRcounts-method Accessor for the counts slot of a MRexperiment object
MRexperiment-class Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments
MRexperiment2biom MRexperiment to biom objects
MRfulltable Table of top microbial marker gene from linear model fit including sequence information
MRtable Table of top microbial marker gene from linear model fit including sequence information
newMRexperiment Create a MRexperiment object
normFactors Access the normalization factors in a MRexperiment object
normFactors-method Access the normalization factors in a MRexperiment object
phenoData Load a clinical/phenotypic dataset associated with a study.
plotBubble Basic plot of binned vectors.
plotClassTimeSeries Plot abundances by class
plotCorr Basic correlation plot function for normalized or unnormalized counts.
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 normalized or unnormalized counts.
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
posteriorProbs-method Access the posterior probabilities that results from analysis
qiimeLoader Load a count dataset associated with a study set up in a Qiime format.
returnAppropriateObj Check if MRexperiment or matrix and return matrix
rowMeans-method Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments
rowSums-method Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments
settings2 Settings for the fitZig function
ssFit smoothing-splines anova fit
ssIntervalCandidate calculate interesting time intervals Calculates time intervals of interest using SS-Anova fitted confidence intervals.
ssPerm class permutations for smoothing-spline time series analysis Creates a list of permuted class memberships for the time series permuation tests.
ssPermAnalysis smoothing-splines anova fits for each permutation
trapz Trapezoidal Integration Compute the area of a function with values 'y' at the points 'x'. Function comes from the pracma package.
uniqueFeatures Table of features unique to a group
zigControl Settings for the fitZig function
[-method Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments