Man pages for BussemakerLab/SelexGLM
Functions for performing feature-based analyis of SELEX-seq data using generalized linear models
| addDdg.N.frame | Calculates nucleotide ddG values from nucleotide design and... |
| addDdg.Shape.frame | Adds window-specific shape ddG contributions for each binding... |
| addDesignMatrix | Add Design Matrix |
| addDesignMatrix.N | Adds design matrix for nucleotide features. |
| addDesignMatrix.Round | Adds design matrix for round features. |
| addDesignMatrix.Shape | Adds design matrix for shape features. |
| addDesignMatrix.View | Adds design matrix for view features. |
| addNddG | Adds nucleotide ddG values for views of DNA probe. |
| addNDesign | Parses probes into nucleotide feature columns to be used in... |
| addNewBetas-Intercept-method | Add New Betas for Intercept |
| addNewBetas-model-method | Add New Betas to model |
| addNewBetas-N-method | Add New Betas to N |
| addNewBetas-Shape-method | Add New Betas to Shape |
| addSeedPsam-set-model-method | Add Seed PSAM |
| addShapeddG | Adds shape ddG values for views of DNA probe. |
| addShapeDesign | Parses probes into shape feature columns to be used in... |
| addShapeValues | Add shape profiles for k-mers. |
| addViewddG | Adds intercept type, view-specific, strand-specific, and... |
| buildNullEquivalenceMatrix-N-method | Build Null Equivalence Matrix for N |
| buildNullEquivalenceMatrix-Shape-method | Build Null Equivalence Matrix for Shape |
| buildRawRegressionFormula | Build Raw Regression Formula |
| buildSymmetricEquivalenceMatrix-N-method | Build Reverse Complement Symmetric Equivalence Matrix for N |
| buildSymmetricEquivalenceMatrix-Shape-method | Build Reverse Complement Symmetric Equivalence Matrix for... |
| cleanAffinityInfo | Removes view-specific affinity scores from data frame. To be... |
| cleanNDesign | Removes nucleotide feature columns used in calculating ddG... |
| cleanShapeDesign | Removes shape feature columns used in calculating ddG values... |
| convertSeq2RegEx | Convert DNA iupac sequence to regular expression |
| countDNAseqLength | Count sequence length of a DNA regular expression. |
| ddg2affinity | Converts view-specific ddG values to affinity scores. |
| featureSet-class | Class 'featureSet' Definition |
| finalizeFeatureBetas-model-method | Finalize Beta Values |
| formatEquivalenceMatrix-N-method | Formats Equivalent Matrix for N |
| formatEquivalenceMatrix-Shape-method | Formats Equivalence matrix for Shape |
| getAffinityType-model-method | Get Affinity Type |
| getConfidenceLevel-model-method | Get Confidence Level |
| getConsensusSeq-model-method | Get Consensus Sequence |
| getDateBetasLastAdded-model-method | Get Date Betas Last Added. |
| getDateInitialized-model-method | Get Date Initialized |
| getDateLastModified-model-method | Get Date Last Modified |
| getDesignMatrix-Intercept-method | Summary of Design Features for Intercept |
| getDesignMatrix-model-method | Get design matrix for all features |
| getDesignMatrix-N-method | Summary Design for Nucleotide Features |
| getDesignMatrix-Shape-method | Design Matrix for Shape Features |
| getDesignMatrixSummary-featureSet-method | Get Design Matrix Summary for featureSet |
| getDownFootprintExtend-featureSet-method | Get Length Downstream Footprint Extension |
| getDownFootprintExtend-model-method | Get Length Downstream Footprint Extension |
| getDownFootprintExtend-N-method | Get Length of Downstream Footprint Extension for Nucleotides |
| getDownFootprintExtend-Shape-method | Get Length (bp) of Downstream Footprint Extension for Shape |
| getEquivMat-N-method | Get equivalence matrix for N |
| getEquivMat-Shape-method | Get Equivalence Matrix for Shape |
| getErrors-Intercept-method | Errors for class Intercept |
| getErrors-N-method | Get beta errors for N |
| getErrors-Shape-method | Get Errors for Shape |
| getExDownBases-model-method | Get Length of Extension Downstream Bases for Shape Parameters |
| getExUpBases-model-method | Get Length of Extension Upstream Bases for Shape Parameters |
| getFeatureDesign-featureSet-method | Get Feature Design for featureSet |
| getFeatureDesign-Intercept-method | Get Feature Design for Intercept |
| getFeatureDesign-model-method | Get Feature Design |
| getFeatureDesign-N-method | Get Feature Design for N |
| getFeatureDesign-Shape-method | Get Feature Design for Shape |
| getFeatures-model-method | Get Features |
| getFpLen-model-method | Get Footprint Length |
| getFpLen-N-method | Get Footprint Length |
| getFpLen-Shape-method | Get Footprint Length for Shape |
| getFsDownFootprintExtend-N-method | Get Length of Upstream Footprint Extension for Full Feature... |
| getFsDownFootprintExtend-Shape-method | Get Length (bp) of Downstream Footprint Extension for Full... |
| getFsUpFootprintExtend-N-method | Get Length of Upstream Footprint Extension for Full Feature... |
| getFsUpFootprintExtend-Shape-method | Get Length (bp) of Upstream Footprint Extension for Full... |
| getGlmFits-featureSet-method | Get 'GlmFits' for class featureSet |
| getIncludeDNAstrand-model-method | Get includeDNAstrand (logical) |
| getIncludeShape-model-method | Get includeShape (logical) |
| getIncludeView-model-method | Get includeView (logical) |
| getIntercept-featureSet-method | Get Intercept for featureSet |
| getIntercept-model-method | Get Intercept |
| getIteration-model-method | Get Iteration |
| getKmerCountAffinities | Create k-mer affinity table for seeding GLM analysis of SELEX... |
| getLeftFixedSeq-model-method | Get Left Fixed Sequence |
| getLeftFixedSeqOverlap-model-method | Get Left Fixed Sequence Overlap |
| getMinAffinity-model-method | Get Minimum Affinity |
| getMinSeedValue-model-method | Get Minimum Seed Value |
| getMissingValueSuppression-model-method | Get Missing Value Suppression Factor |
| getName-model-method | Get Name Slot. |
| getN-featureSet-method | Get N for featureSet |
| getN-model-method | Get N |
| getNumViews-featureSet-method | Get Number of Views for featureSet |
| getNumViews-model-method | Get Number of Views per Strand |
| getOldErrors-Intercept-method | Errors for Previous Iterations for Intercept |
| getOldErrors-N-method | Get beta errors from previous iterations for N |
| getOldErrors-Shape-method | Get Errors from previous iterations for Shape |
| getOldSig-Intercept-method | P-values for Previous Iterations for class Intercept |
| getOldSig-N-method | Get beta p-values from previous iterations for N |
| getOldSig-Shape-method | Get P-values from previous iterations for Shape |
| getOldValues-Intercept-method | Values for previous iterations for Intercept |
| getOldValues-N-method | Get beta values from previous iterations for N |
| getOldValues-Shape-method | Get Values from previous iterations for Shape |
| getOldZ-Intercept-method | Z-scores for Previous Iterations for Intercept |
| getOldZ-N-method | Get beta z-scores from previous iterations for N |
| getOldZ-Shape-method | Get Z-scores from previous iterations for Shape |
| getPlotValues-Intercept-method | Gets Plot Values for Intercept. |
| getPlotValues-N-method | Gets plot values for N |
| getPlotValues-Shape-method | Get Plot Values for Shape |
| getPositions-N-method | Get Positions for Mononucleotides Fitting |
| getPositions-Shape-method | Get positions for Shape Parameter Fitting from Shape |
| getProbeCounts | Build Probe Count Table |
| getPSAM-model-method | Get Mononucleotide PSAM |
| getPSAM-N-method | Get Mononucleotide PSAM. |
| getRcSymmetric-featureSet-method | Get Reverse Complement Symmetric (logical) |
| getRcSymmetric-model-method | Get Reverse Complement Symmetric (logical) |
| getRegions | Get data.frame demarcating regions for a ggplot object. |
| getRegressionFormula-model-method | Get Regression Formula |
| getRightFixedSeq-model-method | Get Right Fixed Sequence |
| getRightFixedSeqOverlap-model-method | Get Right Fixed Sequence Overlap |
| getRoundDesign | Summary of rounds design features |
| getRounds-featureSet-method | Get Rounds |
| getRounds-model-method | Get Rounds |
| getSeedLen-featureSet-method | Get Seed Length for featureSet |
| getSeedLen-model-method | Get Seed Length |
| getSeedLen-N-method | Get Seed Length |
| getSeedLen-Shape-method | Seed Length for Shape |
| getShape-featureSet-method | Get Shape for featureSet |
| getShape-model-method | Get Shape |
| getShapeParamsUsed-featureSet-method | Get Shape Parameters Used |
| getShapeParamsUsed-model-method | Get Shape Parameters Used |
| getShapeParamsUsed-Shape-method | Get Shape Parameters Used from Shape |
| getShapeTable-model-method | Get Shape Table |
| getSig-Intercept-method | P-values for class Intercept |
| getSig-N-method | Get beta p-values for N |
| getSig-Shape-method | Get P-values for Shape |
| getTopRatioLabels | Get sequence labels for psam ratio plot. |
| getTopSeqLabels-N-method | Get Plot Labels for N Plot |
| getUpFootprintExtend-featureSet-method | Get Length Upstream Footprint Extension |
| getUpFootprintExtend-model-method | Get Length Upstream Footprint Extension |
| getUpFootprintExtend-N-method | Get Length of Upstream Footprint Extension for Nucleotides |
| getUpFootprintExtend-Shape-method | Get Length (bp) of Upstream Footprint Extension for Shape |
| getUseFixedValuesOffset.N-model-method | Get useFixedValuesOffset.N (logical) |
| getUseFixedValuesOffset.Shape-model-method | Get useFixedValuesOffset.Shape (logical) |
| getValues-Intercept-method | Values for Intercept |
| getValues-N-method | Get beta values for N |
| getValues-Shape-method | Get Values for Shape |
| getVarRegLen-model-method | Get Variable Region Length |
| getVerbose-model-method | Get Verbose (logical) |
| getZ-Intercept-method | Z-scores for class Intercept |
| getZ-N-method | Get beta z-scores for class N |
| getZ-Shape-method | Get Z-scores for Shape |
| g_legend | Extract ggplot legend. |
| initialize-featureSet-method | Initialize object of class featureSet. |
| initialize-Intercept-method | Constructor for Intercept Class |
| initialize-model-method | Initialize object of class 'model' |
| initialize-N-method | Constructor for S4 class 'N' |
| initialize-Shape-method | Constructor for S4 class 'Shape' |
| Intercept-class | 'Intercept' Class Definition |
| iterateSelexGLM | Iterates Selex GLM Algorithm |
| length-featureSet-method | Length of featureSet |
| length-Intercept-method | Length for Intercept |
| length-model-method | Length of model |
| length-N-method | Length method for N |
| length-Shape-method | Length Method for Shape |
| model-class | Class model for SelexGLM |
| N-class | Class 'N' for Mononucleotide Features |
| NRLBtools | SelexGLM: Utitilies for fitting generalized linear models to... |
| N.validity | Validity Function for N |
| plotBasicIntercept | Plot simple intercept -ddG value for object of class... |
| plot-Intercept-ANY-method | Plot Intercept Plots object of class Intercept with specific... |
| plot-model-ANY-method | Plot model Plots object of class model for any combination of... |
| plot-N-ANY-method | Returns Standardized PSAM Plot for N |
| plotPSAM | Plot PSAM |
| plotPSAMComp.Ratios | Dot plot of ratios between nucleotide psams from 2 objects of... |
| plotPSAMComp.Scatter | Scatter plot showing nucleotide ddG values from 'model1' vs.... |
| plotRounds | Plot round-specific -ddG values for object of class Intercept |
| plot-Shape-ANY-method | Plot Shape |
| plotStrands | Plot Strand Offsets for Intercept |
| plotViews | Plot View-specific ddG contributions for object of class... |
| plotZs-Shape-method | Plot Z-scores for Shape |
| print-featureSet-method | Print method for featureSet |
| print-Intercept-method | Print Method for Intercept |
| print-model-method | Print model |
| print-N-method | Print method for N |
| print-Shape-method | Print Method for Shape |
| revComp | Gets reverse complement of DNA sequence in iupac or regular... |
| scoreKmers | Score K-mer Sequences |
| seedTable2psam-model-method | Build Seed PSAM |
| setAffinityType-set-model-method | Set Affinity Type |
| setConfidenceLevel-set-model-method | Set Confidence Level |
| setConsensusSeq-set-model-method | Set Consensus Sequence |
| setDateBetasLastAdded-set-model-method | Set Date Betas Last Added |
| setDateInitialized-set-model-method | Set Date Initialized |
| setDateLastModified-set-model-method | Set Date Last Modified |
| setDesignMatrixSummary-set-featureSet-method | Set Design Matrix Summary for featureSet |
| setDownFootprintExtend-set-featureSet-method | Set Length Downstream Footprint Extension |
| setDownFootprintExtend-set-model-method | Set Length Downstream Footprint Extension |
| setDownFootprintExtend-set-N-method | Set Length of Downstream Footprint Extension for Nucleotides |
| setDownFootprintExtend-set-Shape-method | Set Length (bp) of Downstream Footprint Extension for Shape |
| setEquivMat-set-N-method | Sets Equivalence Matrix for N |
| setEquivMat-set-Shape-method | Sets Equivalence Matrix for Shape |
| setErrors-set-Intercept-method | Set Errors for Intercept |
| setErrors-set-N-method | Set Errors for N |
| setErrors-set-Shape-method | Set Errors for Shape |
| setExDownBases-set-model-method | Set Length of Extension Downstream Bases for Shape Parameters |
| setExUpBases-set-model-method | Set Length of Extension Upstream Bases for Shape Parameters |
| setFeatures-set-model-method | Set Features |
| setFpLen-set-model-method | Set Footprint Length |
| setFpLen-set-N-method | Set Footprint Length |
| setFpLen-set-Shape-method | Set Footprint Length for Shape |
| setFsDownFootprintExtend-set-N-method | Set Length of Downstream Footprint Extension for Full Feature... |
| setFsDownFootprintExtend-set-Shape-method | Set Length (bp) of Downstream Footprint Extension for Full... |
| setFsUpFootprintExtend-set-N-method | Set Length of Upstream Footprint Extension for Full Feature... |
| setFsUpFootprintExtend-set-Shape-method | Set Length (bp) of Upstream Footprint Extension for Full... |
| setGlmFits-set-featureSet-method | Set 'GlmFits' for class featureSet |
| setIncludeDNAstrand-set-model-method | Set includeDNAstrand (logical) |
| setIncludeShape-set-model-method | Set includeShape (logical) |
| setIncludeView-set-model-method | Set includeView (logical) |
| setIntercept-set-featureSet-method | Set Intercept for class featureSet |
| setIntercept-set-model-method | Set Intercept |
| setIteration-set-model-method | Set Iteration |
| setLeftFixedSeqOverlap-set-model-method | Set Left Fixed Sequence Overlap |
| setLeftFixedSeq-set-model-method | Set Left Fixed Sequence |
| setMinAffinity-set-model-method | Set Minimum Affinity |
| setMinSeedValue-set-model-method | Set Minimum Seed Value |
| setMissingValueSuppression-set-model-method | Set Missing Value Suppression Factor |
| setName-set-model-method | Sets name slot. |
| setN-set-featureSet-method | Set N for class featureSet |
| setN-set-model-method | Set N |
| setNumViews-set-featureSet-method | Set Number of Views for featureSet |
| setNumViews-set-model-method | Set Number of Views per Strand |
| setOldErrors-set-Intercept-method | Set Errors for Previous Iterations for Intercept |
| setOldErrors-set-N-method | Set Errors for Previous Iterations for N |
| setOldErrors-set-Shape-method | Set Errors for Previous Iterations for Shape |
| setOldSig-set-Intercept-method | Set P-values for Previous Iterations for Intercept |
| setOldSig-set-N-method | Set P-values for Previous Iterations for N |
| setOldSig-set-Shape-method | Set P-values from Previous Iterations for Shape |
| setOldValues-set-Intercept-method | Set Values for Previous Iterations for Intercept |
| setOldValues-set-N-method | Set Values for Previous Iterations for N |
| setOldValues-set-Shape-method | Set Values for Previous Iterations for Shape |
| setOldZ-set-Intercept-method | Set Z-scores for Previous Iterations for Intercept |
| setOldZ-set-N-method | Set Z-scores for Previous Iterations for N |
| setOldZ-set-Shape-method | Set Z-scores for Previous Iterations for Shape |
| set_panel_size | Set ggplot panel size |
| setPositions-set-N-method | Set Positions for Mononucleotides for N |
| setPositions-set-Shape-method | Set positions for Shape Parameter Fitting from Shape |
| setRcSymmetric-set-featureSet-method | Set Reverse Complement Symmetry (logical) |
| setRcSymmetric-set-model-method | Set Reverse Complement Symmetric (logical) |
| setRegressionFormula-set-model-method | Set Regression Formula |
| setRightFixedSeqOverlap-set-model-method | Set Right Fixed Sequence Overlap |
| setRightFixedSeq-set-model-method | Set Right Fixed Sequence |
| setRounds-set-featureSet-method | Set Rounds for featureSet |
| setRounds-set-model-method | Set Rounds |
| setSeedLen-set-featureSet-method | Set Seed Length for featureSet |
| setSeedLen-set-model-method | Set Seed Length |
| setSeedLen-set-N-method | Set Seed Length |
| setSeedLen-set-Shape-method | Set Seed Length for Shape |
| setShapeParamsUsed-set-featureSet-method | Set Shape Parameters Used for featureSet |
| setShapeParamsUsed-set-model-method | Set Shape Parameters Used |
| setShapeParamsUsed-set-Shape-method | Set Shape Parameters Used for Shape |
| setShape-set-featureSet-method | Set Shape for class featureSet |
| setShape-set-model-method | Set Shape |
| setShapeTable-set-model-method | Set Shape Table |
| setSig-set-Intercept-method | Set P-values for Intercept |
| setSig-set-N-method | Set P-values for N |
| setSig-set-Shape-method | Set P-values for Shape |
| setUpFootprintExtend-set-featureSet-method | Set Length Upstream Footprint Extension |
| setUpFootprintExtend-set-model-method | Set Length Upstream Footprint Extension |
| setUpFootprintExtend-set-N-method | Set Length of Upstream Footprint Extension for Nucleotides |
| setUpFootprintExtend-set-Shape-method | Set Length (bp) of Upstream Footprint Extension for Shape |
| setUseFixedValuesOffset.N-set-model-method | Set 'useFixedValuesOffset.N' (logical) |
| setUseFixedValuesOffset.Shape-set-model-method | Set useFixedValuesOffset.Shape (logical) |
| setValues-set-Intercept-method | Set Values for class Intercept |
| setValues-set-N-method | Set Values for N |
| setValues-set-Shape-method | Set Values for Shape |
| setVarRegLen-set-model-method | Set Variable Region Length. |
| setVerbose-set-model-method | Set verbose (logical) |
| setZ-set-Intercept-method | Set Z-scores for Intercept |
| setZ-set-N-method | Set Z-scores for N |
| setZ-set-Shape-method | Set Z-scores for Shape |
| Shape-class | Class 'Shape' for Shape Feature Coefficients |
| shapePlotRows | Get Number of Rows for Shape Plot |
| shapeXlabSpacing | Get Spacing for X-labels for Shape Plot |
| show-featureSet-method | Show method for class 'featureSet' |
| show-Intercept-method | Show Method for Intercept |
| show-model-method | Show model |
| show-N-method | Show method for N |
| show-Shape-method | Show method for Shape |
| summary-featureSet-method | Summary Method for featureSet |
| summary-Intercept-method | Summary Method for Intercept |
| summary-model-method | Summary method for model |
| summary-N-method | Summary method for N |
| summary-Shape-method | Summary method for Shape |
| testNBetaSymmetry | Test Symmetry of Nucleotide Betas |
| testShapeBetaSymmetry | Test Symmetry of Shape Betas |
| testViewBetaSymmetry | Test Symmetry of View Betas |
| topModelMatch | Finds Top Match View on Probe for Model. |
| updatedRegressionFormula | Get Updated Regression Formula |
| updateErrors-set-Intercept-method | Update Errors for Intercept |
| updateErrors-set-N-method | Update Errors for N |
| updateErrors-set-Shape-method | Update Errors for Shape |
| updateSig-set-Intercept-method | Update P-values for Intercept |
| updateSig-set-N-method | Update P-values for class N |
| updateSig-set-Shape-method | Update P-values for class Shape |
| updateValues-set-Intercept-method | Update Values for Intercept |
| updateValues-set-N-method | Update Values for N |
| updateValues-set-Shape-method | Update Values for Shape |
| updateZ-set-Intercept-method | Update Z-scores for Intercept |
| updateZ-set-N-method | Update Z-scores for N |
| updateZ-set-Shape-method | Update Z-scores for Shape |
| validFeatureSet | Validity Function for featureSet |
| validIntercept | Validity Function for Intercept |
| validModel | Validity Function for model |
| validShape | Validity Function for Shape |
| verticalPlot_height | Get Vertical Plot Height for object of class model |
| yMarg | Get y-axis plotting margins |
