beadsRR: Beads-only round robin

In athchen/beer: Bayesian Enrichment Estimation in R

Beads-only round robin

Description

To approximate the false positive rate of each approach, each beads-only sample is run individually against all other samples. For BEER, this means that the sample to be compared is encoded as an actual sample, and prior parameters for beads-only samples are re-estimated. Thus, the beads-only round robin also serves to assess how similar the beads-only samples are to one another.

Usage

beadsRR(object, method, BPPARAM = BiocParallel::bpparam(), ...)

Arguments

object	PhIPData object
method	one of 'beer' or 'edgeR' specifying which method to use.
BPPARAM	[BiocParallel::BiocParallelParam] passed to BiocParallel functions.
...	parameters passed to the method specific functions. See the Details section below for additional information.

Details

If method == 'beer', then valid parameters include prior.params, beads.args, jags.params, sample.dir, assay.names, and summarize. A description of the first four parameters can be found in brew. summarize is a logical value indicating whether a PhIPData object with the summarized results should be returned. When running beadsRR, summarize typically does not need to be changed.

When method == 'edgeR', threshold.cpm, threshold.prevalence, and assay.names are valid additional parameters that can be supplied to beadsRR. See edgeR for additional details on each of these parameters.

Value

a PhIPData object

See Also

brew for BEER parameters, edgeR for edgeR parameters, and [BiocParallel::BiocParallelParam] for parallelization.

Examples

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

beadsRR(sim_data, method = "beer")
beadsRR(sim_data, method = "edgeR")
beadsRR(sim_data, method = "edgeR", de.method = "glmQLFTest")

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