collapseDegCreToGene to run much faster. No longer accepts a useParallel argument. Does not use BiocParallel.convDegCreResListToCreGeneScoreGR that called a deprecated function.collapseDegCreToGene to faster running code.collapseDegCreToGene.runDegCre now accepts "qvalue" as an input to pAdjMethod which is now the default. Our testing shows that this method improves the performance of DegCre predictions. The qvalue calculation does not require the user to specify a alphaVal.
Added new function collapseDegCreToGene which converts DegCre results for gene with multiple TSSs to use only the association that spans the shortest distance.
Added new function calcAssocProbOR that calculates the odds-ratio for DegCre association probabilities. This function can operate on assocProb or rawAssocProb values by altering the type flag. It is meant to replace calcRawAssocProbOR.
Added new function convDegCreResListToCreGeneScoreGR that converts DegCre results to a simplified GRanges with the predicted gene and score as metadata.
runDegCre code to use more subfunctions.makePlotGInter to return a sorted GInteractions to avoid inconsistent returns.minNDegs to optimizeAlphaDegCre to stop it from trying testedAlphaVals that result in the number of passing DEGs to be too low for the optimization algorithm to function properly.Updated to use R 4.4.0
Added importFrom for grDevices and utils
Fixed typos in help files
Numerous code style changes made to comply with Bioconductor standards.
Updated to run require R 4.3.3
Vignette style changed to Bioconductor
Selective imports implemented
getAssocDistHits is now exported.calcBinomFDRperBin to give FDR = 1 for 0 assocProbs in top 10 CRE p-values.optimizeAlphaDegCreplotDegCreAssocProbVsDistplotBrowserDegCreNEWS file to track changes.