dot-edgeRBeadsQLF: Estimate edgeR dispersion parameters from the beads-only...

In athchen/beer: Bayesian Enrichment Estimation in R

Estimate edgeR dispersion parameters from the beads-only samples using Cox-Reid profile adjusted likelihood method for estimating dispersions.

Description

Wrapper function to estimate edgeR dispersion parameters from beads-only samples. Peptides can be pre-filtered based on a minimum read count per million (cpm) and the proportion of beads-only samples that surpass the cpm threshold.

Usage

.edgeRBeadsQLF(object, threshold.cpm = 0, threshold.prevalence = 0)

Arguments

object	PhIPData object (can have actual serum samples)
threshold.cpm	CPM threshold to be considered present in a sample
threshold.prevalence	proportion of beads-only samples that surpass threshold.cpm.

Value

a DGEList object with common, trended, and tagwise dispersion estimates

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