# Transcript mapping with high-density oligonucleotide tiling arrays

## Documentation for package ‘tilingArray’ version 1.22.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

tilingArray-package | tilingArray package overview
BGindex | Find the index of the exact match (PM) or background probes from a probeAnno environment
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 an oligonucleotide microarray
otherStrand | Return the name of the opposite strand
plot,segmentation,ANY-method | The class segmentation represents a segmentation result.
plotAlongChrom | Plot signals and segmentation for a region of a chromosome
plotAlongChromLegend | Plot a legend for genomic features
plotFeatures | Plot genomic features for a region along a chromosome
plotPenLL | Plot the log-likelihood and penalized log-likelihoods (AIC, BIC)
plotSegmentationDots | Plot points for a region along a chromosome
plotSegmentationHeatmap | Plot a heatmap diagram for a region along a chromosome
PMindex | Find the index of the exact match (PM) or background probes from a probeAnno environment
posMin | Find the smallest positive number in a vector
qcPlots | Generate simple diagnostic plots for Affymetrix tiling array data
readCel2eSet | Read celfiles into an ExpressionSet object.
residuals.breakpointsPretend | Accessor methods for breakpointsPretend objects - not to be called by the user.
sampleStep | Sampling of ascending numbers to ensure minimal spacing.
segChrom | Fit a piecewise constant curve to along chromosome data (wrapper function)
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