# MicroArray Chromosome Analysis Tool

## Documentation for package ‘macat’ version 1.14.0

## 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
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
getResults | Access results of 'evalScoring'
getsteps | Smooth expression values or scores
kernelize | Smooth expression values or scores
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 Microarray Data from St.Jude Children Research Hospital (USA)