Package 'metagenomeSeq' - Bioconductor

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30 MRexperimentMRexperimentClass "MRexperiment" – a modified eSet object for the data from highthroughputsequencing experimentsDescriptionThis is the main class for metagenomeSeq.Objects from the ClassExtendsObjects should be created with calls to newMRexperiment.Class eSet (package ’Biobase’), directly. Class VersionedBiobase (package ’Biobase’), by class"eSet", distance 2. Class Versioned (package ’Biobase’), by class "eSet", distance 3.MethodsNoteClass-specific methods.[,: Subset operation, taking two arguments and indexing the sample andvariable. Returns an MRexperiment object, including relevant metadata. Setting drop=TRUEgenerates an error. Subsetting the data, the experiment summary slot is repopulated and pDatais repopulated after calling factor (removing levels not present).Note: This is a summary for reference. For an explanation of the actual usage, see the vignette.MRexperiments are the main class in use by metagenomeSeq. The class extends eSet and providesadditional slots which are populated during the analysis pipeline.MRexperiment dataset are created with calls to newMRexperiment. MRexperiment datasets containraw count matrices (integers) accessible through MRcounts. Similarly, normalized count matricescan be accessed (following normalization) through MRcounts by calling norm=TRUE. Followingan analysis, a matrix of posterior probabilities for counts is accessible through posterior.probs.The normalization factors used in analysis can be recovered by normFactors, as can the librarysizes of samples (depths of coverage), libSize.Similarly to other RNASeq bioconductor packages available, the rows of the matrix correspondto a feature (be it OTU, species, gene, etc.) and each column an experimental sample. Pertinentclinical information and potential confounding factors are stored in the phenoData slot (accessedvia pData).To populate the various slots in an MRexperiment several functions are run. 1) cumNormStat calculatesthe proper percentile to calculate normalization factors. The cumNormStat slot is populated.2) cumNorm calculates the actual normalization factors using p = cumNormStat.Other functions will place subsequent matrices (normalized counts (cumNormMat), posterior probabilities(posterior.probs))
MRexperiment2biom 31As mentioned above, MRexperiment is derived from the virtual class,eSet and thereby has a phenoDataslot which allows for sample annotation. In the phenoData data frame factors are stored. The normalizationfactors and library size information is stored in a slot called expSummary that is anannotated data frame and is repopulated for subsetted data.Examples# See vignetteMRexperiment2biomMRexperiment to biom objectsDescriptionWrapper to convert MRexperiment objects to biom objects.UsageMRexperiment2biom(obj, id = NULL, norm = FALSE, log = FALSE, sl = 1000)ArgumentsobjidnormlogslThe MRexperiment object.Optional id for the biom matrix.Normalized data?Logged data?scaling factor for normalized counts.ValueA biom object.See Alsoload_meta load_phenoData newMRexperiment load_biom biom2MRexperiment
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Page 5 and 6: calculateEffectiveSamples 5ValueA M
Page 7 and 8: cumNorm 7ArgumentsValueobjmethodalt
Page 9 and 10: cumNormStat 9cumNormStatCumulative
Page 11 and 12: doEStep 11ArgumentszymmCountstillAc
Page 13 and 14: exportMat 13See AlsofitZigexportMat
Page 15 and 16: filterData 15Author(s)Joseph N. Pau
Page 17 and 18: fitMeta 17fitMetaComputes a slightl
Page 19 and 20: getCountDensity 19See AlsocumNorm z
Page 21 and 22: getPi 21ArgumentszMatrix (m x n) of
Page 23 and 24: libSize 23ArgumentsepstolstillActiv
Page 25 and 26: load_metaQ 25ValueA list with objec
Page 27 and 28: makeLabels 27Referenceshttp://www.n
Page 29: MRcounts 29Examplesdata(lungData)k
Page 33 and 34: MRtable 33See AlsofitZig MRcoefs MR
Page 35 and 36: normFactors 35ArgumentscountsphenoD
Page 37 and 38: plotFeature 37plotFeatureBasic plot
Page 39 and 40: plotMRheatmap 39Examplesdata(mouseD
Page 41 and 42: plotOTU 41plotOTUBasic plot functio
Page 43 and 44: posterior.probs 43posterior.probsAc
Page 45 and 46: Index∗Topic packagemetagenomeSeq-

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