# MicroArray Chromosome Analysis Tool

## Documentation for package `macat' version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

buildMACAT | Create MACAT list from objects in workspace
compute.sliding | Compute and plot smoothing of expression values or scores along the chromosome
discreteKernelize | Discretize and smooth expression values
discretize | Discretize expression values
discretize.tscores | Discretize regularized t-scores
discretizeAll | Discretize complete expression matrix
discretizeAllClasses.tscores | Discretize regularized t-scores
discretizeChromosome | Discretize expression values
discretizeOne | Discretize expression values
evalScoring | Score differential expression, assess significance, and smooth scores along the chromosome
evaluateParameters | Evaluate Performance of Kernel Parameters by Cross-validation
get.results | Access results of 'evalScoring'
getsteps | Smooth expression values or scores
kernelize | Smooth expression values or scores
kernelizeAll | Smooth expression data for all chromosomes
kernelizeToPython | Smooth expression values and write to file
kernelmatrix | Smooth expression values or scores
Loader | Read in data and produce MACAT list
MACATData | Read in data and produce MACAT list
MACATinput | Read in data and produce MACAT list
plot.MACATevalScoring | Plot function for MACATevalScoring objects.
plot.MACATevP | Evaluate Performance of Kernel Parameters by Cross-validation
plotSliding | Compute and plot smoothing of expression values or scores along the chromosome
preprocessedLoader | Read in data and produce MACAT list
scoring | Compute (regularized) t-scores for gene expression data
stjd | Subset Microarry Data from St.Jude Children Research Hospital (USA)