Package 'metagenomeSeq' - Bioconductor

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8 cumNormMatSee AlsofitZig cumNormStatExamplesdata(mouseData)cumNorm(mouseData)head(normFactors(mouseData))cumNormMatCumulative sum scaling factors.DescriptionCalculates each column’s quantile and calculates the sum up to and including that quantile.UsagecumNormMat(obj, p = cumNormStatFast(obj), sl = 1000)ArgumentsobjpslA MRexperiment object.The pth quantile.The value to scale by (default=1000).ValueReturns a matrix normalized by scaling counts up to and including the pth quantile.See AlsofitZig cumNormExamplesdata(mouseData)head(cumNormMat(mouseData))
cumNormStat 9cumNormStatCumulative sum scaling percentile selectionDescriptionCalculates the percentile for which to sum counts up to and scale by. cumNormStat might bedeprecated one day.UsagecumNormStat(obj, qFlag = TRUE, pFlag = FALSE, rel = 0.1, ...)ArgumentsobjqFlagpFlagrelA MRexperiment object.Flag to either calculate the proper percentile using R’s step-wise quantile functionor approximate function.Plot the relative difference of the median deviance from the reference.Cutoff for the relative difference from one median difference from the referenceto the next... Applicable if pFlag == TRUE. Additional plotting parameters.ValuePercentile for which to scale dataSee AlsofitZig cumNorm cumNormStatFastExamplesdata(mouseData)p = round(cumNormStat(mouseData,pFlag=FALSE),digits=2)
Page 1: Package ‘metagenomeSeq’May 22,
Page 5 and 6: calculateEffectiveSamples 5ValueA M
Page 7: cumNorm 7ArgumentsValueobjmethodalt
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 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-

Package 'metagenomeSeq' - Bioconductor

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