Package 'metagenomeSeq' - Bioconductor

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34 newMRexperimentgroupeffnumberEfffileOne of three choices, 0,1,2,3,4. 0: the sort is ordered by a decreasing absolutevalue coefficient fit. 1: the sort is ordered by the raw coefficient fit in decreasingorder. 2: the sort is ordered by the raw coefficient fit in increasing order. 3:the sort is ordered by the p-value of the coefficient fit in increasing order. 4: nosorting.Restrict samples to have at least a "eff" quantile or number of effective samples.Boolean, whether eff should represent quantile (default/FALSE) or number.Name of file, including location, to save the table.ValueTable of the top-ranked features determined by the linear fit’s coefficient.See AlsofitZig MRcoefsExamplesdata(lungData)k = grep("Extraction.Control",pData(lungData)$SampleType)lungTrim = lungData[,-k]k = which(rowSums(MRcounts(lungTrim)>0)
normFactors 35ArgumentscountsphenoDatafeatureDatalibSizenormFactorsA matrix or data frame of count data. The count data is representative of thenumber of reads annotated for a feature (be it gene, OTU, species, etc). Rowsshould correspond to features and columns to samples.An AnnotatedDataFrame with pertinent sample information.An AnnotatedDataFrame with pertinent feature information.libSize, library size, is the total number of reads for a particular sample.normFactors, the normalization factors used in either the model or as scalingfactors of sample counts for each particular sample.DetailsValueSee MRexperiment-class and eSet (from the Biobase package) for the meaning of the variousslots.an object of class MRexperimentAuthor(s)Joseph N Paulson, jpaulson@umiacs.umd.eduExamplescnts = matrix(abs(rnorm(1000)),nc=10)obj
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 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 and 30: MRcounts 29Examplesdata(lungData)k
Page 31 and 32: MRexperiment2biom 31As mentioned ab
Page 33: MRtable 33See AlsofitZig MRcoefs MR
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-

Package 'metagenomeSeq' - Bioconductor

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