aggregateBySample {metagenomeSeq} | R Documentation |
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.
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)