MicrobiomeExperiment: The MicrobiomeExperiment representation class

In HCBravoLab/metagenomeSE:

Description

SummarizedExperiment-like class for microbiome data. rowData is a MicrobiomeFeatures object LINK so it includes: a taxonomy table (DataFrame), #' optional phylogentic tree (phylo object), and a sequence database.

Usage

MicrobiomeExperiment(assays = SimpleList(), rowData = MicrobiomeFeatures(),
  ...)

Details

It supports (most) of the interface to phyloseq objects

Examples

library(metagenomeFeatures)
data(mock_mgF)

sampleNames <- letters[1:4]
pd <- DataFrame(a=letters[1:4], b=1:4)
numcounts <- nrow(mock_mgF) * 4
counts <- matrix(sample(1:1000,numcounts,replace=TRUE), nr=nrow(mock_mgF), nc=4)

MicrobiomeExperiment(assays=SimpleList(counts=counts),
rowData=mock_mgF,
colData=pd
)

HCBravoLab/metagenomeSE documentation built on May 17, 2019, 6:19 p.m.