A B C D E F G I L M N P Q R S T U W Z misc
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 | 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 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 |
extractMR | Extract the essentials of an MRexperiment. |
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 |
fitFeatureModelResults-class | Class "fitFeatureModelResults" - a formal class for storing results from a fitFeatureModel call |
fitLogNormal | Computes a log-normal linear model and permutation based p-values. |
fitMeta | Depcrecated functions in the metagenomeSeq package. |
fitMultipleTimeSeries | Discover differentially abundant time intervals for all bacteria |
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. |
fitZigResults-class | Class "fitZigResults" - a formal class for storing results from a fitZig call |
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 | Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments |
libSize<- | Replace the library sizes in a MRexperiment object |
libSize<--method | 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 Qiime format. |
loadPhenoData | Load a clinical/phenotypic dataset associated with a study. |
load_biom | Depcrecated functions in the metagenomeSeq package. |
load_meta | Depcrecated functions in the metagenomeSeq package. |
load_metaQ | Depcrecated functions in the metagenomeSeq package. |
load_phenoData | Depcrecated functions in the metagenomeSeq package. |
lungData | OTU abundance matrix of samples from a smoker/non-smoker study |
makeLabels | Function to make labels simpler |
mergeMRexperiments | Merge two MRexperiment objects together |
mergeTable | Merge two tables |
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 |
MRihw | MRihw runs IHW within a MRcoefs() call |
MRihw-method | MRihw runs IHW within a MRcoefs() call |
MRihw-method | MRihw runs IHW within a MRcoefs() call |
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 | Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments |
normFactors<- | Replace the normalization factors in a MRexperiment object |
normFactors<--method | Replace 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 |
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 MRexperiment that can be plotted with metavizr |
uniqueFeatures | Table of features unique to a group |
wrenchNorm | Computes normalization factors using wrench instead of cumNorm |
zigControl | Settings for the fitZig function |
[-method | Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments |