gen.syn.dat: Generate Example Microbiome Data

In hk1785/MiVT: Microbiome Virtual Twins

Generate Example Microbiome Data

Description

This function generates example synthetic data that are required to use MiVT.

Usage

gen.syn.dat(tree, tax.tab, prop, disp, num.sams = 50, seq.depth = sample(10000:1e+05, 50), keep.cut.off = 200)

Arguments

tree	A rooted phylogenetic tree.
tax.tab	A taxonomic table where rows are features (OTUs or ASVs), and columns are seven taxonomic ranks (Kingdom, Phylum, Class, Order, Family, Genus, Species)
prop	A vector of proportion parameters for the Dirichlet-Multinomial distribution.
disp	A dispersion parameter for the Dirichlet-Multinomial distribution.
num.sams	A sample size (Default: 50).
seq.depth	A vector of total read counts across subjects (Default: sample(10000:1e+05, 50)).
keep.cut.off	A number of features to keep in the microbiome data (=< 755) (Default: 200).

Value

A synthetic microbiome data in phyloseq format.

Author(s)

Hyunwook Koh

Examples

data(fit)
data(tree)
data(tax.tab)

prop <- fit$pi
disp <- fit$theta

sim.biom <- gen.syn.dat(tree = tree, tax.tab = tax.tab, prop = prop, disp = disp)
sim.biom

hk1785/MiVT documentation built on Dec. 21, 2024, 1:08 p.m.