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

View source: R/edgeR.R

edgeROneQLFR Documentation

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.