dot-getABEdgeR: Derive beta shape parameters using edgeR dispersion estimates

In athchen/beer: Bayesian Enrichment Estimation in R

Derive beta shape parameters using edgeR dispersion estimates

Description

Given a PhIPData object, beads-only shape parameters are estimated by first deriving the peptide-specific edgeR dispersion estimate φ^{edgeR}. φ^{edgeR} corresponds to the squared coefficient of variation for the proportion of reads pulled for a given peptide. Using φ^{edgeR} to derive an estimate of the variance for the proportion of reads pulled by a single peptide, the mean and variance are converted to shape parameters of a beta distribution.

Usage

.getABEdgeR(
  object,
  threshold.cpm = 0,
  threshold.prevalence = 0,
  lower = 1,
  upper = Inf
)

Arguments

object	a PhIPData object.
threshold.cpm	CPM threshold to be considered present in a sample.
threshold.prevalence	proportion of beads-only samples that surpass threshold.cpm.
lower	minimum value of the beta shape parameters.
upper	maximum value of the beta shape parameters.

Value

dataframe with rows corresponding to peptides and columns corresponding to estimated shape parameters of the beta distribution.

See Also

[.edgeRBeads()] for estimating φ^{edgeR}

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