Probabilistic association of DEGs to CREs from differential data

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Documentation for package ‘DegCre’ version 1.5.1

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

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