setParams: Set parameters for different distributions

In lichen-lab/powmic: powmic: an R package for power assessment in microbiome case-control

Set parameters for different distributions

Description

Four functions for setting parameters for different distributions including Negative Binomial Distribution (NB), Zero-Inflated Negative Binomial Distribution (ZINB), Zero-Inflated Poisson Distribution (ZIP) and Dirichlet-Multinomial Distribution (DM)

Usage

setParams.NB(nTaxa=1000,p.DA=0.05,Sigma=Sigma,lmu0=lmu0,lphi0=lphi0,lfc.mu=2,depth=1,sim.seed=123456)
                        
setParams.ZINB(nTaxa=1000,p.DA=0.05,Sigma=Sigma,lmu0=lmu0,lphi0=lphi0,lp0=lp0,lfc.mu=2,depth=1,sim.seed=123456)

setParams.ZIP(nTaxa=1000,p.DA=0.05,Sigma=Sigma,lmu0=lmu0,lp0=lp0,lfc.mu=2,depth=1,sim.seed=123456) 

setParams.DM(nTaxa=1000,p.DA=0.05,lmu0=lmu0,lphi0=lphi0,lfc.mu=2,libsize=5000,depth=1,sim.seed=123456)
                        

Arguments

nTaxa	Number of Taxa in the simulation. If Sigma is not NULL, nTaxa equals to the dimension of Sigma
p.DA	Proportion of Differential Abundant (DA) Taxa
Sigma	Estimated microbial correlation matrix when the distribution is "NB", ZINB" or "ZIP"
lmu0	logarithmic mean abundance parameter
lphi0	logarithmic dispersion parameter
lp0	logarithmic zero-inflated probability when the distribution is "ZINB" and "ZIP"
lfc.mu	logarithmic fold change of DA Taxa. Default is 2
depth	Depth factor. depth is multiplied to lmu0 to increase the library size
libsize	Sequence depth when the distribution is "DM"
sim.seed	Simulation seed. Default is 123456

Value

A list containing all parameters in the arguments

Examples

## Not run: 
 library(powmic)
 distrib='NB'
 setParams=switch(distrib,ZIP=setParams.ZIP, NB=setParams.NB, ZINB=setParams.ZINB)
 data(params)
 lmu0=log(params$mu)
 lphi0=log(params$phi)
 Sigma=params$Sigma
 sim.params=setParams(Sigma=Sigma,lmu0=lmu0,lphi0=lphi0)
 
## End(Not run)

lichen-lab/powmic documentation built on April 7, 2023, 4:40 p.m.