aggregateBySample: Aggregates a MRexperiment object or counts matrix to by a...

In HCBravoLab/metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

Aggregates a MRexperiment object or counts matrix to by a factor.

Description

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.

Usage

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

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

Arguments

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'

Value

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

Examples

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)

HCBravoLab/metagenomeSeq documentation built on March 17, 2024, 3:21 p.m.