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 |

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