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CHANGES IN VERSION 1.1.1

  • Version up.

CHANGES IN VERSION 1.1.0.9000

NEW FEATURES

  • 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.

OTHER CHANGES

  • Streamlined runDegCre code to use more subfunctions.

BUG FIXES

  • Changed the internal function makePlotGInter to return a sorted GInteractions to avoid inconsistent returns.

CHANGES IN VERSION 1.0.2

  • Changed citation to Genome Research article

BUG FIXES

  • Added parameter 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.

CHANGES IN VERSION 0.99.16

  • Added utils to DESCRIPTION

CHANGES IN VERSION 0.99.15

  • Updated to use R 4.4.0

  • Added importFrom for grDevices and utils

  • Fixed typos in help files

CHANGES IN VERSION 0.99.14

BUG FIXES

  • Added imported packages to DESCRIPTION

CHANGES IN VERSION 0.99.13

  • 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

CHANGES IN VERSION 0.99.12

BUG FIXES

  • Fixed one more bad href in help files.

CHANGES IN VERSION 0.99.11

BUG FIXES

  • Fixed bad hrefs in help files.

CHANGES IN VERSION 0.99.10

BUG FIXES

  • Fixed example for runDegCre.

CHANGES IN VERSION 0.99.9

BUG FIXES

  • Fixed test functions to subset GRanges.

CHANGES IN VERSION 0.99.8

BUG FIXES

  • Fixed runnable examples to load GenomicRanges.

CHANGES IN VERSION 0.99.7

BUG FIXES

  • Changed test functions to run on chr1 only for efficiency.

CHANGES IN VERSION 0.99.6

BUG FIXES

  • Changed examples to run on chr1 for computational efficiency.

CHANGES IN VERSION 0.99.4

BUG FIXES

  • Fixed F to FALSE in example

CHANGES IN VERSION 0.99.3

BUG FIXES

  • Set all non-exported functions to not run examples.
  • Fixed vignette code.

NEW FEATURES

  • getAssocDistHits is now exported.

CHANGES IN VERSION 0.99.2

BUG FIXES

  • Fixed calcAUC.Rd to not run example.

CHANGES IN VERSION 0.99.1

BUG FIXES

  • Fixed calcBinomFDRperBin to give FDR = 1 for 0 assocProbs in top 10 CRE p-values.

CHANGES IN VERSION 0.99.0

BUG FIXES

  • Added missing unit test for optimizeAlphaDegCre

CHANGES IN VERSION 0.3.0

NEW FEATURES

  • Added unit tests for most functions.

BUG FIXES

  • Fixed row names in plotDegCreAssocProbVsDist
  • Changed left margin handling and arched plot color bar placement in plotBrowserDegCre
  • Added internal keyword to un-exported functions.

CHANGES IN VERSION 0.2.0

NEW FEATURES

  • Added a NEWS file to track changes.
  • Made numerous style changes to code in preparation for Bioconductor submission.