ZIPG (version 1.1)

ZIPG_main: Fit zero-inflated poisson-gamma model via EM Algorithm

Description

Fit zero-inflated poisson-gamma model via EM Algorithm

Usage

ZIPG_main(
  data,
  W,
  M,
  X,
  X_star,
  return_model = TRUE,
  pbWald_list = NULL,
  bWald_list = NULL
)

Value

A list of ZIPG fitted model. Use ZIPG_summary() for a quick look at the results.

Arguments

data

Data.frame for covariates of interest

W

Count data

M

Sequencing depth, ZIPG use log(M) as offset by default

X

Formula of covariates of differential abundance

X_star

Formula of covariates of differential varibility

return_model

whether return full complete imfomation for fitted model

pbWald_list

A list of arguments for parameteric bootstrap Wald test, B for bootstrap sample size, X0 and X_star0 for formula of covariates included in H0

bWald_list

A list of arguments for non-parameteric bootstrap Wald test, B for bootstrap sample size,

Examples

data(Dietary)
dat = Dietary
ZIPG_res <- ZIPG_main(data = dat$COV,
X = ~ALC01+nutrPC1+nutrPC2, X_star = ~ ALC01,
W = dat$OTU[,100], M = dat$M )
ZIPG_summary(ZIPG_res)