Entry: buildMACAT
Aliases: buildMACAT
Keywords: file
Description: Create MACAT list from objects in workspace
URL: ../../../library/macat/html/buildMACAT.html

Entry: compute.sliding
Aliases: compute.sliding plotSliding
Keywords: manip
Description: Compute and plot smoothing of expression values or scores along the chromosome
URL: ../../../library/macat/html/compute.sliding.html

Entry: discreteKernelize
Aliases: discreteKernelize
Keywords: manip
Description: Discretize and smooth expression values
URL: ../../../library/macat/html/discreteKernelize.html

Entry: discretize
Aliases: discretize discretizeChromosome discretizeOne
Keywords: manip
Description: Discretize expression values
URL: ../../../library/macat/html/discretize.html

Entry: discretize.tscores
Aliases: discretize.tscores discretizeAllClasses.tscores
Keywords: manip
Description: Discretize regularized t-scores
URL: ../../../library/macat/html/discretize.tscores.html

Entry: discretizeAll
Aliases: discretizeAll
Keywords: manip
Description: Discretize complete expression matrix
URL: ../../../library/macat/html/discretizeAll.html

Entry: evalScoring
Aliases: evalScoring
Keywords: manip
Description: Score differential expression, assess significance, and smooth scores along the chromosome
URL: ../../../library/macat/html/evalScoring.html

Entry: evaluateParameters
Aliases: evaluateParameters plot.MACATevP
Keywords: manip
Description: Evaluate Performance of Kernel Parameters by Cross-validation
URL: ../../../library/macat/html/evaluateParameters.html

Entry: getResults
Aliases: getResults
Keywords: manip
Description: Access results of 'evalScoring'
URL: ../../../library/macat/html/get.results.html

Entry: html
Aliases: myhtml getHtml
Keywords: internal
Description: HTML functions for MACAT.
URL: ../../../library/macat/html/html.html

Entry: kernelize
Aliases: kernelmatrix getsteps kernelize
Keywords: manip
Description: Smooth expression values or scores
URL: ../../../library/macat/html/kernelize.html

Entry: kernelizeAll
Aliases: kernelizeAll
Keywords: manip
Description: Smooth expression data for all chromosomes
URL: ../../../library/macat/html/kernelizeAll.html

Entry: kernelizeToPython
Aliases: kernelizeToPython
Keywords: manip
Description: Smooth expression values and write to file
URL: ../../../library/macat/html/kernelizeToPython.html

Entry: Kernels
Aliases: kNN rbf basePairDistance fitkernelparams kernels
Keywords: internal
Description: various kernel functions for computations in MACAT
URL: ../../../library/macat/html/kernels.html

Entry: loaddatapkg
Aliases: loaddatapkg
Keywords: internal
Description: Load data package
URL: ../../../library/macat/html/loaddatapkg.html

Entry: Auxiliary Computation Functions
Aliases: squaredDist maxDistances pair.distances toPython rawDataToPython saveForPython slidingAverageAt compare.gammas getExpressionByChromosome.MACATData getExpressionByClass.MACATData getExpression.MACATData getExpressionByProbeset.MACATData demo.part crossvalParam evalParams
Keywords: internal
Description: Auxiliary Functions for Computations in MACAT
URL: ../../../library/macat/html/macat-internal.html

Entry: plot.MACATevalScoring
Aliases: plot.MACATevalScoring
Keywords: hplot
Description: Plot function for MACATevalScoring objects.
URL: ../../../library/macat/html/plot.MACATevalScoring.html

Entry: preprocessedLoader
Aliases: preprocessedLoader Loader MACATinput MACATData
Keywords: file
Description: Read in data and produce MACAT list
URL: ../../../library/macat/html/preprocessedLoader.html

Entry: Python data format
Aliases: pydata pythondata
Keywords: internal
Description: Flat file format
URL: ../../../library/macat/html/pythondata.html

Entry: scoring
Aliases: scoring
Keywords: manip
Description: Compute (regularized) t-scores for gene expression data
URL: ../../../library/macat/html/scoring.html

Entry: stjd
Aliases: stjd
Keywords: datasets
Description: Subset Microarry Data from St.Jude Children Research Hospital (USA)
URL: ../../../library/macat/html/stjd.html
