Package 'metagenomeSeq' - Bioconductor

4 biom2MRexperimentUsageaggregateByTaxonomy(obj, lvl, alternate = FALSE, norm = FALSE,log = FALSE, aggfun = colSums, sl = 1000, out = "MRexperiment")aggTax(obj, lvl, alternate = FALSE, norm = FALSE, log = FALSE,aggfun = colSums, sl = 1000, out = "MRexperiment")ArgumentsobjlvlalternatenormlogaggfunA MRexperiment object or count matrix.featureData column name from the MRexperiment object or if count matrix objecta vector of labels.Use the rowname for undefined OTUs instead of aggregating to "no_match".Whether to aggregate normalized counts or not.Whether or not to log2 transform the counts - if MRexperiment object.Aggregation function.sl scaling value, default is 1000.outEither ’MRexperiment’ or ’matrix’ValueAn aggregated count matrix.Examples# not run# aggregateByTaxonomy(mouseData,lvl="genus",norm=TRUE,aggfun=colMedians)# aggTax(mouseData,lvl=phylum,norm=FALSE,aggfun=colSums)biom2MRexperimentBiome to MRexperiment objectsDescriptionWrapper to convert biome files to MRexperiment objects.Usagebiom2MRexperiment(obj)ArgumentsobjThe biome object file.