Man pages for athchen/beer
Bayesian Enrichment Estimation in R
| beadsRR | Beads-only round robin |
| beer-package | beer: an R package for quantifying antibody reactivities for... |
| brew | Bayesian Enrichment Estimation in R (BEER) |
| brewOne | Run BEER for one sample |
| dot-beadsRRBeer | Function to run the beads-only round robin using BEER |
| dot-beadsRREdgeR | Function to run the beads-only round robin using edgeR |
| dot-brewSamples | Run BEER for all samples |
| dot-checkCounts | Function to check that the counts matrix only contains... |
| dot-checkOverwrite | Function to check whether an assay will be overwritten |
| dot-edgeRBeads | Estimate edgeR dispersion parameters from the beads-only data... |
| dot-edgeRBeadsQLF | Estimate edgeR dispersion parameters from the beads-only... |
| dot-getABEdgeR | Derive beta shape parameters using edgeR dispersion estimates |
| dot-getABMLE | Wrapper function to derive MLE estimates of a, b from... |
| dot-getABMLEProp | Helper function to derive MLE estimates of a, b from a vector... |
| dot-getABMOM | Wrapper function to derive MOM estimates of a, b from... |
| dot-getABMOMProp | Helper function to derive MOM estimates of a, b from a vector... |
| dot-guessEnrichedEdgeR | Guess super-enriched peptides based on edgeR fold-change... |
| dot-guessEnrichedMLE | Guess enriched peptides based on MLE estimates of the true... |
| dot-tidyAssayNames | Clean-up specified assay names |
| dot-tidyInputsJAGS | Clean inputs for JAGS parameters |
| dot-tidyInputsPrior | Clean up inputs for prior estimation |
| dot-tidyInputsSE | Clean up inputs for identifying super-enriched peptides |
| edgeROne | Run edgeR for one sample against all the beads-only samples. |
| edgeROneQLF | Run edgeR for one sample against all the beads-only samples... |
| 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... |
| summarizeRunOne | Derive point estimates for c, pi, phi, and Z for a particular... |
