runEdgeR: Run edgeR on PhIP-Seq data

In athchen/beer: Bayesian Enrichment Estimation in R

Run edgeR on PhIP-Seq data

Description

Run edgeR on PhIP-Seq data

Usage

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

Arguments

object	PhIPData object
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
beadsRR	logical value specifying whether each beads-only sample should be compared to all other beads-only samples.
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

PhIPData object with log2 estimated fold-changes and p-values for enrichment stored in the assays specified by 'assay.names'.

See Also

[BiocParallel::BiocParallelParam], beadsRR

Examples

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

## Default back-end evaluation
runEdgeR(sim_data)

## Serial
runEdgeR(sim_data, BPPARAM = BiocParallel::SerialParam())

## Snow
runEdgeR(sim_data, BPPARAM = BiocParallel::SnowParam())

## With glmQLFTest
runEdgeR(sim_data, de.method = "glmQLFTest")

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