Files in BussemakerLab/SelexGLM
Functions for performing feature-based analyis of SELEX-seq data using generalized linear models
DESCRIPTION
NAMESPACE
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
build/vignette.rds
inst/doc/HowToFitMononucleotideModel.R
inst/doc/HowToFitMononucleotideModel.Rmd
inst/doc/HowToFitMononucleotideModel.html
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
