dot-brewSamples: Run BEER for all samples

In athchen/beer: Bayesian Enrichment Estimation in R

Run BEER for all samples

Description

Encapsulated function to run each sample against all beads-only samples. The code is wrapped in this smaller function to (1) modularize the code and (2) make sure the cli output colors don't change.

Usage

.brewSamples(
  object,
  sample.id,
  beads.id,
  se.matrix,
  prior.params,
  beads.prior,
  beads.args,
  jags.params,
  tmp.dir,
  BPPARAM
)

Arguments

object	PhIPData object
sample.id	vector of sample IDs to iterate over
beads.id	vector of IDs corresponding to beads-only samples
se.matrix	matrix indicating which peptides are clearly enriched
prior.params	list of prior parameters
beads.prior	data frame of beads-only prior parameters
beads.args	named list of parameters supplied to estimating beads-only prior parameters (a_0, b_0)
jags.params	list of JAGS parameters
tmp.dir	directory to store JAGS samples
BPPARAM	[BiocParallel::BiocParallelParam] passed to BiocParallel functions.

Value

vector of process id's for internal checking of whether functions were parallelized correctly.

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