SimDirFactorContour: Generate synthetic OTU abundance table from DirFactor model...

In boyuren158/DirFactor: Dependent Dirichlet processes factor model for nonparametric ordination fo microbiome data

Description

Generate synthetic OTU abundance table from DirFactor model with two biological sample clusters.

Usage

SimDirFactorContour(strength, vcounts, n, p, m, hyper)

Arguments

strength	Required. A positive scalar. Determine the distance between the centroids of two clusters. Larger value means larger separation.
vcounts	Required. A vector of total counts per biological sample. Example: vcounts=c(1e5,1e6).
n	Required. Number of biological samples in the simualted table.
p	Required. Number of species in the simulated dataset.
m	Required. True number of factors in the simulated dataset.
hyper	Required. A list of hyper-parameters in the priors. See Details in DirFactor for the fields in this list.

Value

A list contains the following fields:

• sigma: a vector with p components of simulated sigma.

• Q: a p*n matrix of normal latent variables.

• X.tru: a m*p matrix of species latent factors.

• Y.tru: a m*n matrix of biological sample latent factors.

• er: a scalar of the simulated pure error.

• data: a list with the same size of vcounts. data[[i]] is the simulated dataset with total counts vcounts[[i]].

Examples

my.hyper = list( nv = 3, a.er = 1, b.er = 0.3, a1 = 3, 
                 a2 = 4, m = 10, alpha = 10, beta = 0 )
SimDirFactorContour( strength = 1, vcounts=c(1e5,1e6), n = 22, p = 68, m = 3, hyper = my.hyper )

boyuren158/DirFactor documentation built on May 13, 2019, 1:38 a.m.