Package 'metagenomeSeq' - Bioconductor

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26 lungDataload_phenoDataLoad a clinical/phenotypic dataset associated with a study.DescriptionLoad a matrix of metadata associated with a study.Usageload_phenoData(file, tran = FALSE, sep = "\t")ArgumentsfiletransepPath and filename of the actual clinical file.Boolean. If the covariates are along the columns and samples along the rows,then tran should equal TRUE.The separator for the file.ValueThe metadata as a dataframe.See Alsoload_metaExamples# see vignettelungDataOTU abundance matrix of samples from a smoker/non-smoker studyDescriptionUsageFormatThis is a list with a matrix of OTU counts,otu names, taxa annotations for each OTU, and phenotypicdata. Samples along the columns and OTUs along the rows.lungDataA list of OTU matrix, taxa, otus, and phenotypes
makeLabels 27Referenceshttp://www.ncbi.nlm.nih.gov/pubmed/21680950makeLabelsFunction to make labels simplerDescriptionBeginning to transition to better axes for plotsUsagemakeLabels(x = "samples", y = "abundance", norm, log)Argumentsxynormlogstring for the x-axisstring for the y-axisis the data normalized?is the data logged?Valuevector of x,y labelsmouseDataOTU abundance matrix of mice samples from a diet longitudinal studyDescriptionUsageFormatThis is a list with a matrix of OTU counts, taxa annotations for each OTU, otu names, and vector ofphenotypic data. Samples along the columns and OTUs along the rows.mouseDataA list of OTU matrix, taxa, otus, and phenotypesReferenceshttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894525/
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: load_metaQ 25ValueA list with objec
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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