Statistical analysis for sparse high-throughput sequencing


[Up] [Top]

Documentation for package ‘metagenomeSeq’ version 1.0.6

Help Pages

aggregateM Aggregates counts by a particular classification.
cumNorm Cumulative sum scaling factors.
cumNormMat Cumulative sum scaling factors.
cumNormStat Cumulative sum scaling percentile selection
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 eSet dataset as a matrix.
exportMatrix export the normalized eSet dataset as a matrix.
exportStats Various statistics of the count data.
expSummary Access MRexperiment object experiment data
expSummary-method Access MRexperiment object experiment data
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_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
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 microbial marker gene from linear model fit
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
MRfisher Wrapper to run fisher's test on presence/absence of a feature.
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.
plotCorr Basic correlation plot function for normalized or unnormalized counts.
plotGenus Basic plot function of the raw or normalized data.
plotMRheatmap Basic heatmap plot function for normalized counts.
plotOTU Basic plot function of the raw or normalized data.
posterior.probs Access the posterior probabilities that results from analysis
posterior.probs-method Access the posterior probabilities that results from analysis
qiimeLoader Load a count dataset associated with a study set up in a Qiime format.
settings Settings for the fitZig function
zigControl Settings for the fitZig function
[-method Class "MRexperiment" - a modified eSet object for the data from high-throughput sequencing experiments