Man pages for HCBravoLab/metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
| 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... |
| fitFeatureModelResults-class | Class "fitFeatureModelResults" - a formal class for storing... |
| 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. |
| fitZigResults-class | Class "fitZigResults" - a formal class for storing results... |
| 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... |
| MRihw | MRihw runs IHW within a MRcoefs() call |
| MRihw-fitFeatureModelResults | MRihw runs IHW within a MRcoefs() call |
| MRihw-fitZigResults | MRihw runs IHW within a MRcoefs() call |
| 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 |
| wrenchNorm | Computes normalization factors using wrench instead of... |
| zigControl | Settings for the fitZig function |
