summarizeRun: Summarize MCMC chain and return point estimates for BEER...

In athchen/beer: Bayesian Enrichment Estimation in R

Summarize MCMC chain and return point estimates for BEER parameters

Description

Posterior means are used as point estimates for c, π, φ, and Z. As super-enriched peptides are tossed out before MCMC sampling, super-enriched peptides return NA for the φ and Z point estimates. Indices corresponding to a particular peptide in the MCMC sampler are mapped back to the original peptide names.

Usage

summarizeRun(
  object,
  jags.files,
  se.matrix,
  burn.in = 0,
  post.thin = 1,
  assay.names = c(phi = NULL, phi_Z = "logfc", Z = "prob", c = "sampleInfo", pi =
    "sampleInfo"),
  BPPARAM = BiocParallel::bpparam()
)

Arguments

object	a PhIPData object
jags.files	list of files containing MCMC sampling results
se.matrix	logical matrix indicating which peptides were identified as super-enriched peptides
burn.in	number of iterations to be burned
post.thin	thinning parameter
assay.names	named vector of specifying where to store point estimates
BPPARAM	[BiocParallel::BiocParallelParam] passed to BiocParallel functions.

Value

PhIPData object with point estimates stored in the assays specified by 'assay.names'.

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