edgeROneQLF: Run edgeR for one sample against all the beads-only samples...

In athchen/beer: Bayesian Enrichment Estimation in R

Run edgeR for one sample against all the beads-only samples using edgeR's QLF Test for differential expression.

Description

This function is not really for external use. It's exported for parallelization purposes. For more detailed descriptions see runEdgeR.

Usage

edgeROneQLF(object, sample, beads, common.disp, tagwise.disp, trended.disp)

Arguments

object	PhIPData object
sample	sample name of the sample to compare against beads-only samples
beads	sample names for beads-only samples
common.disp	edgeR estimated common dispersion parameter
tagwise.disp	edgeR estimated tagwise dispersion parameter
trended.disp	edgeR estimated trended dispersion parameter

Value

list with sample name, log2 fc estimate, and log10 p-value

Examples

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

beads_disp <- beer:::.edgeRBeadsQLF(sim_data)
edgeROneQLF(
    sim_data, "9", colnames(sim_data)[sim_data$group == "beads"],
    beads_disp$common.dispersion, beads_disp$tagwise.disp,
    beads_disp$trended.disp
)

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