brewOne: Run BEER for one sample

In athchen/beer: Bayesian Enrichment Estimation in R

Run BEER for one sample

Description

This function is not really for external use. It's exported for parallelization purposes. For more detailed descriptions see brew.

Usage

brewOne(
  object,
  sample,
  prior.params,
  n.chains = 1,
  n.adapt = 1000,
  n.iter = 10000,
  thin = 1,
  na.rm = TRUE,
  ...,
  seed = as.numeric(format(Sys.Date(), "%Y%m%d"))
)

Arguments

object	PhIPData object
sample	sample name
prior.params	vector of prior parameters
n.chains	number of chains to run
n.adapt	number of iterations to use as burn-in.
n.iter	number of iterations for the MCMC chain to run (after n.adapt)
thin	thinning parameter
na.rm	what to do with NA values (for JAGS)
...	extra parameters for JAGS
seed	number/string for reproducibility purposes.

Value

nothing, saves the the results to an RDS in either a temp directory or the specified directory.

Examples

sim_data <- readRDS(system.file("extdata", "sim_data.rds", package = "beer"))

beads_prior <- getAB(subsetBeads(sim_data), "edgeR")
brewOne(sim_data, "9", list(
    a_0 = beads_prior[["a_0"]],
    b_0 = beads_prior[["b_0"]],
    a_pi = 2, b_pi = 300,
    a_phi = 1.25, b_phi = 0.1,
    a_c = 80, b_c = 20,
    fc = 1
))

athchen/beer documentation built on July 2, 2022, 10:35 p.m.