Probabilistic association of DEGs to CREs from differential data
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Documentation for package ‘DegCre’ version 1.3.0
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 |