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

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315
Source code
23
Man pages
309
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BussemakerLab/SelexGLM: Functions for performing feature-based analyis of SELEX-seq data using generalized linear models
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API

API for BussemakerLab/SelexGLM
Functions for performing feature-based analyis of SELEX-seq data using generalized linear models

Global functions
Intercept Man page
Intercept-class Man page
N Man page
N-class Man page
N.validity Man page
NRLBtools Man page
NRLBtools-package Man page
Shape Man page
Shape-class Man page
addDdg.N.frame Man page
addDdg.Shape.frame Man page
addDesignMatrix Man page
addDesignMatrix.N Man page
addDesignMatrix.Round Man page
addDesignMatrix.Shape Man page
addDesignMatrix.View Man page
addNDesign Man page
addNddG Man page
addNewBetas,Intercept-method Man page
addNewBetas,N-method Man page
addNewBetas,Shape-method Man page
addNewBetas,model-method Man page
addSeedPsam<-,model-method Man page
addShapeDesign Man page
addShapeValues Man page
addShapeddG Man page
addViewddG Man page
buildNullEquivalenceMatrix,N-method Man page
buildNullEquivalenceMatrix,Shape-method Man page
buildRawRegressionFormula Man page
buildSymmetricEquivalenceMatrix,N-method Man page
buildSymmetricEquivalenceMatrix,Shape-method Man page
cleanAffinityInfo Man page
cleanNDesign Man page
cleanShapeDesign Man page
convertSeq2RegEx Man page
countDNAseqLength Man page
ddg2affinity Man page
featureSet Man page
featureSet-class Man page
finalizeFeatureBetas,model-method Man page
formatEquivalenceMatrix,N-method Man page
formatEquivalenceMatrix,Shape-method Man page
g_legend Man page
getAffinityType,model-method Man page
getConfidenceLevel,model-method Man page
getConsensusSeq,model-method Man page
getDateBetasLastAdded,model-method Man page
getDateInitialized,model-method Man page
getDateLastModified,model-method Man page
getDesignMatrix,Intercept-method Man page
getDesignMatrix,N-method Man page
getDesignMatrix,Shape-method Man page
getDesignMatrix,model-method Man page
getDesignMatrixSummary,featureSet-method Man page
getDownFootprintExtend,N-method Man page
getDownFootprintExtend,Shape-method Man page
getDownFootprintExtend,featureSet-method Man page
getDownFootprintExtend,model-method Man page
getEquivMat,N-method Man page
getEquivMat,Shape-method Man page
getErrors,Intercept-method Man page
getErrors,N-method Man page
getErrors,Shape-method Man page
getExDownBases,model-method Man page
getExUpBases,model-method Man page
getFeatureDesign,Intercept-method Man page
getFeatureDesign,N-method Man page
getFeatureDesign,Shape-method Man page
getFeatureDesign,featureSet-method Man page
getFeatureDesign,model-method Man page
getFeatures,model-method Man page
getFpLen,N-method Man page
getFpLen,Shape-method Man page
getFpLen,model-method Man page
getFsDownFootprintExtend,N-method Man page
getFsDownFootprintExtend,Shape-method Man page
getFsUpFootprintExtend,N-method Man page
getFsUpFootprintExtend,Shape-method Man page
getGlmFits,featureSet-method Man page
getIncludeDNAstrand,model-method Man page
getIncludeShape,model-method Man page
getIncludeView,model-method Man page
getIntercept,featureSet-method Man page
getIntercept,model-method Man page
getIteration,model-method Man page
getKmerCountAffinities Man page
getLeftFixedSeq,model-method Man page
getLeftFixedSeqOverlap,model-method Man page
getMinAffinity,model-method Man page
getMinSeedValue,model-method Man page
getMissingValueSuppression,model-method Man page
getN,featureSet-method Man page
getN,model-method Man page
getName,model-method Man page
getNumViews,featureSet-method Man page
getNumViews,model-method Man page
getOldErrors,Intercept-method Man page
getOldErrors,N-method Man page
getOldErrors,Shape-method Man page
getOldSig,Intercept-method Man page
getOldSig,N-method Man page
getOldSig,Shape-method Man page
getOldValues,Intercept-method Man page
getOldValues,N-method Man page
getOldValues,Shape-method Man page
getOldZ,Intercept-method Man page
getOldZ,N-method Man page
getOldZ,Shape-method Man page
getPSAM,N-method Man page
getPSAM,model-method Man page
getPlotValues,Intercept-method Man page
getPlotValues,N-method Man page
getPlotValues,Shape-method Man page
getPositions,N-method Man page
getPositions,Shape-method Man page
getProbeCounts Man page
getRcSymmetric,featureSet-method Man page
getRcSymmetric,model-method Man page
getRegions Man page
getRegressionFormula,model-method Man page
getRightFixedSeq,model-method Man page
getRightFixedSeqOverlap,model-method Man page
getRoundDesign Man page
getRounds,featureSet-method Man page
getRounds,model-method Man page
getSeedLen,N-method Man page
getSeedLen,Shape-method Man page
getSeedLen,featureSet-method Man page
getSeedLen,model-method Man page
getShape,featureSet-method Man page
getShape,model-method Man page
getShapeParamsUsed,Shape-method Man page
getShapeParamsUsed,featureSet-method Man page
getShapeParamsUsed,model-method Man page
getShapeTable,model-method Man page
getSig,Intercept-method Man page
getSig,N-method Man page
getSig,Shape-method Man page
getTopRatioLabels Man page
getTopSeqLabels,N-method Man page
getUpFootprintExtend,N-method Man page
getUpFootprintExtend,Shape-method Man page
getUpFootprintExtend,featureSet-method Man page
getUpFootprintExtend,model-method Man page
getUseFixedValuesOffset.N,model-method Man page
getUseFixedValuesOffset.Shape,model-method Man page
getValues,Intercept-method Man page
getValues,N-method Man page
getValues,Shape-method Man page
getVarRegLen,model-method Man page
getVerbose,model-method Man page
getZ,Intercept-method Man page
getZ,N-method Man page
getZ,Shape-method Man page
initialize,Intercept-method Man page
initialize,N-method Man page
initialize,Shape-method Man page
initialize,featureSet-method Man page
initialize,model-method Man page
iterateSelexGLM Man page
length,Intercept-method Man page
length,N-method Man page
length,Shape-method Man page
length,featureSet-method Man page
length,model-method Man page
model Man page
model-class Man page
plot,Intercept,ANY-method Man page
plot,N,ANY-method Man page
plot,Shape,ANY-method Man page
plot,model,ANY-method Man page
plotBasicIntercept Man page
plotPSAM Man page
plotPSAMComp.Ratios Man page
plotPSAMComp.Scatter Man page
plotRounds Man page
plotStrands Man page
plotViews Man page
plotZs,Shape-method Man page
print,Intercept-method Man page
print,N-method Man page
print,Shape-method Man page
print,featureSet-method Man page
print,model-method Man page
revComp Man page
scoreKmers Man page
seedTable2psam,model-method Man page
setAffinityType<-,model-method Man page
setConfidenceLevel<-,model-method Man page
setConsensusSeq<-,model-method Man page
setDateBetasLastAdded<-,model-method Man page
setDateInitialized<-,model-method Man page
setDateLastModified<-,model-method Man page
setDesignMatrixSummary<-,featureSet-method Man page
setDownFootprintExtend<-,N-method Man page
setDownFootprintExtend<-,Shape-method Man page
setDownFootprintExtend<-,featureSet-method Man page
setDownFootprintExtend<-,model-method Man page
setEquivMat<-,N-method Man page
setEquivMat<-,Shape-method Man page
setErrors<-,Intercept-method Man page
setErrors<-,N-method Man page
setErrors<-,Shape-method Man page
setExDownBases<-,model-method Man page
setExUpBases<-,model-method Man page
setFeatures<-,model-method Man page
setFpLen<-,N-method Man page
setFpLen<-,Shape-method Man page
setFpLen<-,model-method Man page
setFsDownFootprintExtend<-,N-method Man page
setFsDownFootprintExtend<-,Shape-method Man page
setFsUpFootprintExtend<-,N-method Man page
setFsUpFootprintExtend<-,Shape-method Man page
setGlmFits<-,featureSet-method Man page
setIncludeDNAstrand<-,model-method Man page
setIncludeShape<-,model-method Man page
setIncludeView<-,model-method Man page
setIntercept<-,featureSet-method Man page
setIntercept<-,model-method Man page
setIteration<-,model-method Man page
setLeftFixedSeq<-,model-method Man page
setLeftFixedSeqOverlap<-,model-method Man page
setMinAffinity<-,model-method Man page
setMinSeedValue<-,model-method Man page
setMissingValueSuppression<-,model-method Man page
setN<-,featureSet-method Man page
setN<-,model-method Man page
setName<-,model-method Man page
setNumViews<-,featureSet-method Man page
setNumViews<-,model-method Man page
setOldErrors<-,Intercept-method Man page
setOldErrors<-,N-method Man page
setOldErrors<-,Shape-method Man page
setOldSig<-,Intercept-method Man page
setOldSig<-,N-method Man page
setOldSig<-,Shape-method Man page
setOldValues<-,Intercept-method Man page
setOldValues<-,N-method Man page
setOldValues<-,Shape-method Man page
setOldZ<-,Intercept-method Man page
setOldZ<-,N-method Man page
setOldZ<-,Shape-method Man page
setPositions<-,N-method Man page
setPositions<-,Shape-method Man page
setRcSymmetric<-,featureSet-method Man page
setRcSymmetric<-,model-method Man page
setRegressionFormula<-,model-method Man page
setRightFixedSeq<-,model-method Man page
setRightFixedSeqOverlap<-,model-method Man page
setRounds<-,featureSet-method Man page
setRounds<-,model-method Man page
setSeedLen<-,N-method Man page
setSeedLen<-,Shape-method Man page
setSeedLen<-,featureSet-method Man page
setSeedLen<-,model-method Man page
setShape<-,featureSet-method Man page
setShape<-,model-method Man page
setShapeParamsUsed<-,Shape-method Man page
setShapeParamsUsed<-,featureSet-method Man page
setShapeParamsUsed<-,model-method Man page
setShapeTable<-,model-method Man page
setSig<-,Intercept-method Man page
setSig<-,N-method Man page
setSig<-,Shape-method Man page
setUpFootprintExtend<-,N-method Man page
setUpFootprintExtend<-,Shape-method Man page
setUpFootprintExtend<-,featureSet-method Man page
setUpFootprintExtend<-,model-method Man page
setUseFixedValuesOffset.N<-,model-method Man page
setUseFixedValuesOffset.Shape<-,model-method Man page
setValues<-,Intercept-method Man page
setValues<-,N-method Man page
setValues<-,Shape-method Man page
setVarRegLen<-,model-method Man page
setVerbose<-,model-method Man page
setZ<-,Intercept-method Man page
setZ<-,N-method Man page
setZ<-,Shape-method Man page
set_panel_size Man page
shapePlotRows Man page
shapeXlabSpacing Man page
show,Intercept-method Man page
show,N-method Man page
show,Shape-method Man page
show,featureSet-method Man page
show,model-method Man page
summary,Intercept-method Man page
summary,N-method Man page
summary,Shape-method Man page
summary,featureSet-method Man page
summary,model-method Man page
testNBetaSymmetry Man page
testShapeBetaSymmetry Man page
testViewBetaSymmetry Man page
topModelMatch Man page
updateErrors<-,Intercept-method Man page
updateErrors<-,N-method Man page
updateErrors<-,Shape-method Man page
updateSig<-,Intercept-method Man page
updateSig<-,N-method Man page
updateSig<-,Shape-method Man page
updateValues<-,Intercept-method Man page
updateValues<-,N-method Man page
updateValues<-,Shape-method Man page
updateZ<-,Intercept-method Man page
updateZ<-,N-method Man page
updateZ<-,Shape-method Man page
updatedRegressionFormula Man page
validFeatureSet Man page
validIntercept Man page
validModel Man page
validShape Man page
verticalPlot_height Man page
yMarg Man page
BussemakerLab/SelexGLM documentation built on May 17, 2019, 5:41 p.m.

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