aggregateBySample: Aggregates a MRexperiment object or counts matrix to by a...
In metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

Description Usage Arguments Value Examples

Using the phenoData information in the MRexperiment, calling aggregateBySample on a MRexperiment and a particular phenoData column (i.e. 'diet') will aggregate counts using the aggfun function (default rowMeans). Possible aggfun alternatives include rowMeans and rowMedians.

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aggregateBySample(obj, fct, aggfun = rowMeans, out = "MRexperiment")

aggSamp(obj, fct, aggfun = rowMeans, out = "MRexperiment")

`obj`	A MRexperiment object or count matrix.
`fct`	phenoData column name from the MRexperiment object or if count matrix object a vector of labels.
`aggfun`	Aggregation function.
`out`	Either 'MRexperiment' or 'matrix'

An aggregated count matrix or MRexperiment object where the new pData is a vector of 'fct' levels.

data(mouseData)
aggregateBySample(mouseData[1:100,],fct="diet",aggfun=rowSums)
# not run
# aggregateBySample(mouseData,fct="diet",aggfun=matrixStats::rowMedians)
# aggSamp(mouseData,fct='diet',aggfun=rowMaxs)