dot-beadsRRBeer: Function to run the beads-only round robin using BEER

In athchen/beer: Bayesian Enrichment Estimation in R

Function to run the beads-only round robin using BEER

Description

Each sample is run in comparison to all other beads-only samples to approximate the false positive rate of detecting enrichments.

Usage

.beadsRRBeer(
  object,
  prior.params = list(method = "edgeR", a_pi = 2, b_pi = 300, a_phi = 1.25, b_phi =
    0.1, a_c = 80, b_c = 20, fc = 1),
  beads.args = list(lower = 1),
  jags.params = list(n.chains = 1, n.adapt = 1000, n.iter = 10000, thin = 1, na.rm =
    TRUE, burn.in = 0, post.thin = 1, seed = as.numeric(format(Sys.Date(), "%Y%m%d"))),
  sample.dir = NULL,
  assay.names = c(phi = NULL, phi_Z = "logfc", Z = "prob", c = "sampleInfo", pi =
    "sampleInfo"),
  summarize = TRUE,
  BPPARAM = bpparam()
)

Arguments

object	PhIPData object
prior.params	named list of prior parameters
beads.args	named list of parameters supplied to estimating beads-only prior parameters (a_0, b_0)
jags.params	named list of parameters for running MCMC using JAGS
sample.dir	path to temporarily store RDS files for each sample run, if NULL then [base::tempdir] is used to temporarily store MCMC output and cleaned afterwards.
assay.names	named vector indicating where MCMC results should be stored in the PhIPData object
summarize	logical indicating whether to return a PhIPData object.
BPPARAM	[BiocParallel::BiocParallelParam] passed to BiocParallel functions.

Value

vector of process IDs or a PhIPData object

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