# Probabilistic association of DEGs to CREs from differential data

## Documentation for package ‘DegCre’ version 1.8.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

DegCre-package | DegCre
calcAssocProbOR | Calculate Odds-ratio
calcRawAssocProbOR | Calculate Raw Association Probability Odds Ratio (OR)
collapseDegCreToGene | Collapse DegCre associations to a single TSS per gene
convDegCreResListToCreGeneScoreGR | Convert a degCreResList to a creGeneScoreGR
convertDegCreDataFrame | Convert DegCre Results List to DataFrame
convertdegCreResListToGInteraction | Convert DegCre Results List to GInteractions Object
DegCre | DegCre
degCrePRAUC | Calculate PR AUC for DegCre results.
DexNR3C1 | DegCre input data for examples.
getAssocDistHits | Get Associations and Distances Between Genomic Regions
getDistBinNullAssocProb | Calculate Null Association Probability for Each Distance Bin
getExpectAssocPerDEG | Get Expected Associations per DEG
optimizeAlphaDegCre | Run DegCre with DEG alpha optimization.
plotBrowserDegCre | Make Browser Plots from DegCre Results
plotDegCreAssocProbVsDist | Plot DegCre Association Probability vs. Binned Genomic Distance
plotDegCreBinHeuristic | Plot DegCre Bin Algorithm Statistics
plotExpectedAssocsPerDeg | Plot Histogram of Expected Associations per DEG
runDegCre | Generate DegCre associations