Bayesian Enrichment Estimation in R

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Documentation for package ‘beer’ version 1.11.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.beadsRRBeer	Function to run the beads-only round robin using BEER
.beadsRREdgeR	Function to run the beads-only round robin using edgeR
.brewSamples	Run BEER for all samples
.checkCounts	Function to check that the counts matrix only contains integers
.checkOverwrite	Function to check whether an assay will be overwritten
.edgeRBeads	Estimate edgeR dispersion parameters from the beads-only data using qCML
.edgeRBeadsQLF	Estimate edgeR dispersion parameters from the beads-only samples using Cox-Reid profile adjusted likelihood method for estimating dispersions.
.getABEdgeR	Derive beta shape parameters using edgeR dispersion estimates
.getABMLE	Wrapper function to derive MLE estimates of a, b from beads-only samples
.getABMLEProp	Helper function to derive MLE estimates of a, b from a vector of proportions
.getABMOM	Wrapper function to derive MOM estimates of a, b from beads-only samples
.getABMOMProp	Helper function to derive MOM estimates of a, b from a vector of proportions
.guessEnrichedEdgeR	Guess super-enriched peptides based on edgeR fold-change estimates
.guessEnrichedMLE	Guess enriched peptides based on MLE estimates of the true fold-change
.tidyAssayNames	Clean-up specified assay names
.tidyInputsJAGS	Clean inputs for JAGS parameters
.tidyInputsPrior	Clean up inputs for prior estimation
.tidyInputsSE	Clean up inputs for identifying super-enriched peptides
beadsRR	Beads-only round robin
brew	Bayesian Enrichment Estimation in R (BEER)
brewOne	Run BEER for one sample
edgeROne	Run edgeR for one sample against all the beads-only samples.
edgeROneQLF	Run edgeR for one sample against all the beads-only samples using edgeR's QLF Test for differential expression.
getAB	Estimate beads-only shape parameters
getBF	Calculate Bayes Factors
getExpected	Calculate expected read counts or proportion of reads
guessEnriched	Identifying clearly enriched peptides
guessInits	Derive initial estimates of unknown model parameters
runEdgeR	Run edgeR on PhIP-Seq data
summarizeRun	Summarize MCMC chain and return point estimates for BEER parameters
summarizeRunOne	Derive point estimates for c, pi, phi, and Z for a particular sample