# Analysis of high-density oligonucleotide tiling arrays

## Documentation for package `tilingArray' version 1.10.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

tilingArray-package | tilingArray package overview
breakpoints.breakpointsPretend | Accessor methods for breakpointsPretend objects - not to be called by the user.
comparisonPlot | Plot a vertical layout of panels for the comparison of different along-chromosome profiles.
confint | The class segmentation represents a segmentation result.
confint,segmentation-method | The class segmentation represents a segmentation result.
costMatrix | Segmentation cost matrix
findSegments | Fit a piecewise constant curve to a sequence of numbers - OBSOLETE, please use function segment instead.
logLik | The class segmentation represents a segmentation result.
logLik,segmentation-method | The class segmentation represents a segmentation result.
normalizeByReference | Probe-specific normalization of hybridization intensities from a short-oligo microarray
otherStrand | Return the name of the opposite strand
plot,segmentation-method | The class segmentation represents a segmentation result.
plotAlongChrom | Plot signals and segmentation along a chromosomal region
posMin | Find the smallest positive number in a vector
readCel2eSet | Read celfiles into an eSet object.
residuals.breakpointsPretend | Accessor methods for breakpointsPretend objects - not to be called by the user.
sampleStep | Sampling of ascending numbers to ensure minimal spacing.
segment | Fit a piecewise constant curve: segmentation by dynamic programming
segmentation-class | The class segmentation represents a segmentation result.
show,segmentation-method | The class segmentation represents a segmentation result.
tilingArray | tilingArray package overview