processPhyloseq {adaptiveGPCA}

Make the input matrices for adaptive gPCA

Description

Takes a phyloseq object and creates the matrices necessary to do adaptive gPCA.

Usage

processPhyloseq(physeq, ca = FALSE)

Arguments

physeq

A phyloseq object, from the phyloseq package.

ca

If TRUE, do the normalization as for correspondence analysis (transform counts to relative abundances, compute sample weights, center the relative abundances according to the sample weights). Otherwise, simply center the data.

Value

A list of the matrix to perform adaptive gPCA on (X), the species similarity matrix (Q), and the sample weights (weights).

Examples

data(AntibioticPhyloseq)
pp = processPhyloseq(AntibioticPhyloseq)