Transcript mapping with high-density oligonucleotide tiling arrays

Documentation for package ‘tilingArray’ version 1.70.0

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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-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.
gffSub	Example of a genomic feature object
logLik	The class segmentation represents a segmentation result.
logLik-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-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.
segnf	Example of a segmentation output object
show-method	The class segmentation represents a segmentation result.
tilingArray	tilingArray package overview