dot-beadsRREdgeR: Function to run the beads-only round robin using edgeR

In athchen/beer: Bayesian Enrichment Estimation in R

Function to run the beads-only round robin using edgeR

Description

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

Usage

.beadsRREdgeR(
  object,
  threshold.cpm = 0,
  threshold.prevalence = 0,
  assay.names = c(logfc = "logfc", prob = "prob"),
  de.method = "exactTest",
  BPPARAM = BiocParallel::bpparam()
)

Arguments

object	A PhIPData object of only beads-only samples.
threshold.cpm	CPM threshold to be considered present in a sample
threshold.prevalence	proportion of beads-only samples that surpass threshold.cpm.
assay.names	named vector specifying the assay names for the log2(fold-change) and exact test p-values. If the vector is not names, the first and second entries are used as defaults.
de.method	character describing which edgeR test for differential expression should be used. Must be one of 'exactTest' or 'glmQLFTest'.
BPPARAM	[BiocParallel::BiocParallelParam] passed to BiocParallel functions.

Value

vector of process IDs

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