metagenomeFeatures (version 1.2.2)

aggregate_taxa: Aggregates a MRexperiment object and returns either an aggregated MRexperiment or counts matrix to a user defined taxonomic level.

Usage

aggregate_taxa(obj, lvl, aggfun = colSums, out = "MRexperiment", ...)

Arguments

obj

A MRexperiment-class object or count matrix.

lvl

featureData column name from the MRexperiment object or if count matrix object a vector of labels.

aggfun

Matrix aggregation function, e.g. colSums.

out

Either 'MRexperiment' or 'matrix'

...

Additional parameters to pass to MRcount, e.g. norm, log, and sl.

Value

• An aggregated count matrix or MRexperiment

Details

Using the featureData information in the MRexperiment-class object, aggregate_taxa aggregates the OTU count data (MRexperiment assaData slot) to a user defined taxonomic level (i.e. 'genus') using the defined aggfun function (default colSums). Possible aggfun alternatives include and column wise matrix calculations, e.g. colMeans, colMedians.

Examples

# not run
# data("mouseData", package = "metagenomeSeq")
# aggregateByTaxonomy(mouseData[1:100,],lvl="class",norm=TRUE,aggfun=colSums)
# aggregateByTaxonomy(mouseData,lvl="class",norm=TRUE,aggfun=colMedians)
# aggTax(mouseData,lvl='phylum',norm=FALSE,aggfun=colSums)