Package 'metagenomeSeq' - Bioconductor

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14 expSummaryexportStatsVarious statistics of the count data.DescriptionUsageA matrix of values for each sample. The matrix consists of sample ids, the sample scaling factor,quantile value, the number identified features, and library size (depth of coverage).exportStats(obj, p = cumNormStat(obj), file = "~/Desktop/res.stats.tsv")ArgumentsobjpfileA MRexperiment object with count data.Quantile value to calculate the scaling factor and quantiles for the various samples.Output file name.ValueNone.See AlsocumNorm quantileExamples# see vignetteexpSummaryAccess MRexperiment object experiment dataDescriptionUsageThe expSummary vectors represent the column (sample specific) sums of features, i.e. the totalnumber of reads for a sample, libSize and also the normalization factors, normFactor.expSummary(obj)Argumentsobja MRexperiment object.
filterData 15Author(s)Joseph N. Paulson, jpaulson@umiacs.umd.eduExamplesdata(mouseData)expSummary(mouseData)filterDataFilter datasets according to no. features present in features with atleast a certain depth.DescriptionFilter the data based on the number of present features after filtering samples by depth of coverage.There are many ways to filter the object, this is just one way.UsagefilterData(obj, present = 1, depth = 1000)ArgumentsobjpresentdepthA MRexperiment object or count matrix.Features with at least ’present’ postive samples.Sampls with at least this much depth of coverageValueA MRexperiment object.Examplesdata(mouseData)filterData(mouseData)
Page 1: Package ‘metagenomeSeq’May 22,
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: exportMat 13See AlsofitZigexportMat
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 and 30: MRcounts 29Examplesdata(lungData)k
Page 31 and 32: MRexperiment2biom 31As mentioned ab
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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