asPhyloseq: Microbiome Phyloseq wrapper for community samples

In gheysenemma/microsimR: A Simulator Package with a collection of basic community models that outputs count data of microbial communities

Description

Takes in samples in vector or matrix format and merges them to a microbiome phyloseq class object.

Usage

asPhyloseq(S, ...)

Arguments

S	Each parameter given to the function is a sample vector or matrix to be merged into one phyloseq object of samples. The vectors/matrices must all contain the same number of species in order to be merged. A phyloseq object requires at least a matrix of min. 2 columns, therefore an error is thrown if only a vector is given without additional vector/matrix objects.
...	vector(s)/matrice(s): see description of S

Details

Requires phyloseq package (Bioconductor). Function will install package when not installed yet.

Value

A microbiome phyloseq class object with species/OTUs as rows and samples as columns.

Examples

## Not run: 
A = powerlawA(n = 80, alpha = 1.6),
glv_timeseries <- glv(N = 80, A = A, tend = 100)
soi_sample <- rmse_sample(soi(N = 80, I = 1000, A = A, tend = 1000))
physeq <- asPhyloseq(glv_timeseries, soi_sample)

## End(Not run)

gheysenemma/microsimR documentation built on Dec. 20, 2021, 10:46 a.m.