Files in BussemakerLab/SelexGLM

Functions for performing feature-based analyis of SELEX-seq data using generalized linear models

R/Intercept-class.R R/Intercept-validity.R R/N-class.R R/N-validity.R R/Shape-class.R R/Shape-validity.R R/addDesignMatrix.R R/buildRawRegressionFormula.R R/dnaSequenceTools.R R/featureSet-class.R R/featureSet-validity.R R/generic-functions-definitions.R R/getKmerCountAffinities.R R/getProbeCounts.R R/iterateSelexGLM.R R/model-class.R R/model-validity.R R/package-SelexGLM.R R/plottingTools.R R/scoreKmers.R R/topModelMatch.R R/updatedRegressionFormula.R inst/doc/HowToFitMononucleotideModel.R inst/doc/HowToFitMononucleotideModel.Rmd man/Intercept-class.Rd man/N-class.Rd man/N.validity.Rd man/NRLBtools.Rd man/Shape-class.Rd man/addDdg.N.frame.Rd man/addDdg.Shape.frame.Rd man/addDesignMatrix.N.Rd man/addDesignMatrix.Rd man/addDesignMatrix.Round.Rd man/addDesignMatrix.Shape.Rd man/addDesignMatrix.View.Rd man/addNDesign.Rd man/addNddG.Rd man/addNewBetas-Intercept-method.Rd man/addNewBetas-N-method.Rd man/addNewBetas-Shape-method.Rd man/addNewBetas-model-method.Rd man/addSeedPsam-set-model-method.Rd man/addShapeDesign.Rd man/addShapeValues.Rd man/addShapeddG.Rd man/addViewddG.Rd man/buildNullEquivalenceMatrix-N-method.Rd man/buildNullEquivalenceMatrix-Shape-method.Rd man/buildRawRegressionFormula.Rd man/buildSymmetricEquivalenceMatrix-N-method.Rd man/buildSymmetricEquivalenceMatrix-Shape-method.Rd man/cleanAffinityInfo.Rd man/cleanNDesign.Rd man/cleanShapeDesign.Rd man/convertSeq2RegEx.Rd man/countDNAseqLength.Rd man/ddg2affinity.Rd man/featureSet-class.Rd man/finalizeFeatureBetas-model-method.Rd man/formatEquivalenceMatrix-N-method.Rd man/formatEquivalenceMatrix-Shape-method.Rd man/g_legend.Rd man/getAffinityType-model-method.Rd man/getConfidenceLevel-model-method.Rd man/getConsensusSeq-model-method.Rd man/getDateBetasLastAdded-model-method.Rd man/getDateInitialized-model-method.Rd man/getDateLastModified-model-method.Rd man/getDesignMatrix-Intercept-method.Rd man/getDesignMatrix-N-method.Rd man/getDesignMatrix-Shape-method.Rd man/getDesignMatrix-model-method.Rd man/getDesignMatrixSummary-featureSet-method.Rd man/getDownFootprintExtend-N-method.Rd man/getDownFootprintExtend-Shape-method.Rd man/getDownFootprintExtend-featureSet-method.Rd man/getDownFootprintExtend-model-method.Rd man/getEquivMat-N-method.Rd man/getEquivMat-Shape-method.Rd man/getErrors-Intercept-method.Rd man/getErrors-N-method.Rd man/getErrors-Shape-method.Rd man/getExDownBases-model-method.Rd man/getExUpBases-model-method.Rd man/getFeatureDesign-Intercept-method.Rd man/getFeatureDesign-N-method.Rd man/getFeatureDesign-Shape-method.Rd man/getFeatureDesign-featureSet-method.Rd man/getFeatureDesign-model-method.Rd man/getFeatures-model-method.Rd man/getFpLen-N-method.Rd man/getFpLen-Shape-method.Rd man/getFpLen-model-method.Rd man/getFsDownFootprintExtend-N-method.Rd man/getFsDownFootprintExtend-Shape-method.Rd man/getFsUpFootprintExtend-N-method.Rd man/getFsUpFootprintExtend-Shape-method.Rd man/getGlmFits-featureSet-method.Rd man/getIncludeDNAstrand-model-method.Rd man/getIncludeShape-model-method.Rd man/getIncludeView-model-method.Rd man/getIntercept-featureSet-method.Rd man/getIntercept-model-method.Rd man/getIteration-model-method.Rd man/getKmerCountAffinities.Rd man/getLeftFixedSeq-model-method.Rd man/getLeftFixedSeqOverlap-model-method.Rd man/getMinAffinity-model-method.Rd man/getMinSeedValue-model-method.Rd man/getMissingValueSuppression-model-method.Rd man/getN-featureSet-method.Rd man/getN-model-method.Rd man/getName-model-method.Rd man/getNumViews-featureSet-method.Rd man/getNumViews-model-method.Rd man/getOldErrors-Intercept-method.Rd man/getOldErrors-N-method.Rd man/getOldErrors-Shape-method.Rd man/getOldSig-Intercept-method.Rd man/getOldSig-N-method.Rd man/getOldSig-Shape-method.Rd man/getOldValues-Intercept-method.Rd man/getOldValues-N-method.Rd man/getOldValues-Shape-method.Rd man/getOldZ-Intercept-method.Rd man/getOldZ-N-method.Rd man/getOldZ-Shape-method.Rd man/getPSAM-N-method.Rd man/getPSAM-model-method.Rd man/getPlotValues-Intercept-method.Rd man/getPlotValues-N-method.Rd man/getPlotValues-Shape-method.Rd man/getPositions-N-method.Rd man/getPositions-Shape-method.Rd man/getProbeCounts.Rd man/getRcSymmetric-featureSet-method.Rd man/getRcSymmetric-model-method.Rd man/getRegions.Rd man/getRegressionFormula-model-method.Rd man/getRightFixedSeq-model-method.Rd man/getRightFixedSeqOverlap-model-method.Rd man/getRoundDesign.Rd man/getRounds-featureSet-method.Rd man/getRounds-model-method.Rd man/getSeedLen-N-method.Rd man/getSeedLen-Shape-method.Rd man/getSeedLen-featureSet-method.Rd man/getSeedLen-model-method.Rd man/getShape-featureSet-method.Rd man/getShape-model-method.Rd man/getShapeParamsUsed-Shape-method.Rd man/getShapeParamsUsed-featureSet-method.Rd man/getShapeParamsUsed-model-method.Rd man/getShapeTable-model-method.Rd man/getSig-Intercept-method.Rd man/getSig-N-method.Rd man/getSig-Shape-method.Rd man/getTopRatioLabels.Rd man/getTopSeqLabels-N-method.Rd man/getUpFootprintExtend-N-method.Rd man/getUpFootprintExtend-Shape-method.Rd man/getUpFootprintExtend-featureSet-method.Rd man/getUpFootprintExtend-model-method.Rd man/getUseFixedValuesOffset.N-model-method.Rd man/getUseFixedValuesOffset.Shape-model-method.Rd man/getValues-Intercept-method.Rd man/getValues-N-method.Rd man/getValues-Shape-method.Rd man/getVarRegLen-model-method.Rd man/getVerbose-model-method.Rd man/getZ-Intercept-method.Rd man/getZ-N-method.Rd man/getZ-Shape-method.Rd man/initialize-Intercept-method.Rd man/initialize-N-method.Rd man/initialize-Shape-method.Rd man/initialize-featureSet-method.Rd man/initialize-model-method.Rd man/iterateSelexGLM.Rd man/length-Intercept-method.Rd man/length-N-method.Rd man/length-Shape-method.Rd man/length-featureSet-method.Rd man/length-model-method.Rd man/model-class.Rd man/plot-Intercept-ANY-method.Rd man/plot-N-ANY-method.Rd man/plot-Shape-ANY-method.Rd man/plot-model-ANY-method.Rd man/plotBasicIntercept.Rd man/plotPSAM.Rd man/plotPSAMComp.Ratios.Rd man/plotPSAMComp.Scatter.Rd man/plotRounds.Rd man/plotStrands.Rd man/plotViews.Rd man/plotZs-Shape-method.Rd man/print-Intercept-method.Rd man/print-N-method.Rd man/print-Shape-method.Rd man/print-featureSet-method.Rd man/print-model-method.Rd man/revComp.Rd man/scoreKmers.Rd man/seedTable2psam-model-method.Rd man/setAffinityType-set-model-method.Rd man/setConfidenceLevel-set-model-method.Rd man/setConsensusSeq-set-model-method.Rd man/setDateBetasLastAdded-set-model-method.Rd man/setDateInitialized-set-model-method.Rd man/setDateLastModified-set-model-method.Rd man/setDesignMatrixSummary-set-featureSet-method.Rd man/setDownFootprintExtend-set-N-method.Rd man/setDownFootprintExtend-set-Shape-method.Rd man/setDownFootprintExtend-set-featureSet-method.Rd man/setDownFootprintExtend-set-model-method.Rd man/setEquivMat-set-N-method.Rd man/setEquivMat-set-Shape-method.Rd man/setErrors-set-Intercept-method.Rd man/setErrors-set-N-method.Rd man/setErrors-set-Shape-method.Rd man/setExDownBases-set-model-method.Rd man/setExUpBases-set-model-method.Rd man/setFeatures-set-model-method.Rd man/setFpLen-set-N-method.Rd man/setFpLen-set-Shape-method.Rd man/setFpLen-set-model-method.Rd man/setFsDownFootprintExtend-set-N-method.Rd man/setFsDownFootprintExtend-set-Shape-method.Rd man/setFsUpFootprintExtend-set-N-method.Rd man/setFsUpFootprintExtend-set-Shape-method.Rd man/setGlmFits-set-featureSet-method.Rd man/setIncludeDNAstrand-set-model-method.Rd man/setIncludeShape-set-model-method.Rd man/setIncludeView-set-model-method.Rd man/setIntercept-set-featureSet-method.Rd man/setIntercept-set-model-method.Rd man/setIteration-set-model-method.Rd man/setLeftFixedSeq-set-model-method.Rd man/setLeftFixedSeqOverlap-set-model-method.Rd man/setMinAffinity-set-model-method.Rd man/setMinSeedValue-set-model-method.Rd man/setMissingValueSuppression-set-model-method.Rd man/setN-set-featureSet-method.Rd man/setN-set-model-method.Rd man/setName-set-model-method.Rd man/setNumViews-set-featureSet-method.Rd man/setNumViews-set-model-method.Rd man/setOldErrors-set-Intercept-method.Rd man/setOldErrors-set-N-method.Rd man/setOldErrors-set-Shape-method.Rd man/setOldSig-set-Intercept-method.Rd man/setOldSig-set-N-method.Rd man/setOldSig-set-Shape-method.Rd man/setOldValues-set-Intercept-method.Rd man/setOldValues-set-N-method.Rd man/setOldValues-set-Shape-method.Rd man/setOldZ-set-Intercept-method.Rd man/setOldZ-set-N-method.Rd man/setOldZ-set-Shape-method.Rd man/setPositions-set-N-method.Rd man/setPositions-set-Shape-method.Rd man/setRcSymmetric-set-featureSet-method.Rd man/setRcSymmetric-set-model-method.Rd man/setRegressionFormula-set-model-method.Rd man/setRightFixedSeq-set-model-method.Rd man/setRightFixedSeqOverlap-set-model-method.Rd man/setRounds-set-featureSet-method.Rd man/setRounds-set-model-method.Rd man/setSeedLen-set-N-method.Rd man/setSeedLen-set-Shape-method.Rd man/setSeedLen-set-featureSet-method.Rd man/setSeedLen-set-model-method.Rd man/setShape-set-featureSet-method.Rd man/setShape-set-model-method.Rd man/setShapeParamsUsed-set-Shape-method.Rd man/setShapeParamsUsed-set-featureSet-method.Rd man/setShapeParamsUsed-set-model-method.Rd man/setShapeTable-set-model-method.Rd man/setSig-set-Intercept-method.Rd man/setSig-set-N-method.Rd man/setSig-set-Shape-method.Rd man/setUpFootprintExtend-set-N-method.Rd man/setUpFootprintExtend-set-Shape-method.Rd man/setUpFootprintExtend-set-featureSet-method.Rd man/setUpFootprintExtend-set-model-method.Rd man/setUseFixedValuesOffset.N-set-model-method.Rd man/setUseFixedValuesOffset.Shape-set-model-method.Rd man/setValues-set-Intercept-method.Rd man/setValues-set-N-method.Rd man/setValues-set-Shape-method.Rd man/setVarRegLen-set-model-method.Rd man/setVerbose-set-model-method.Rd man/setZ-set-Intercept-method.Rd man/setZ-set-N-method.Rd man/setZ-set-Shape-method.Rd man/set_panel_size.Rd man/shapePlotRows.Rd man/shapeXlabSpacing.Rd man/show-Intercept-method.Rd man/show-N-method.Rd man/show-Shape-method.Rd man/show-featureSet-method.Rd man/show-model-method.Rd man/summary-Intercept-method.Rd man/summary-N-method.Rd man/summary-Shape-method.Rd man/summary-featureSet-method.Rd man/summary-model-method.Rd man/testNBetaSymmetry.Rd man/testShapeBetaSymmetry.Rd man/testViewBetaSymmetry.Rd man/topModelMatch.Rd man/updateErrors-set-Intercept-method.Rd man/updateErrors-set-N-method.Rd man/updateErrors-set-Shape-method.Rd man/updateSig-set-Intercept-method.Rd man/updateSig-set-N-method.Rd man/updateSig-set-Shape-method.Rd man/updateValues-set-Intercept-method.Rd man/updateValues-set-N-method.Rd man/updateValues-set-Shape-method.Rd man/updateZ-set-Intercept-method.Rd man/updateZ-set-N-method.Rd man/updateZ-set-Shape-method.Rd man/updatedRegressionFormula.Rd man/validFeatureSet.Rd man/validIntercept.Rd man/validModel.Rd man/validShape.Rd man/verticalPlot_height.Rd man/yMarg.Rd vignettes/HowToFitMononucleotideModel.Rmd