Entry: PMindex
Aliases: PMindex BGindex
Keywords: manip
Description: Find the index of the exact match (PM) or background probes from a probeAnno environment
URL: ../../../library/tilingArray/html/PMindex.html

Entry: breakpointsPretend
Aliases: residuals.breakpointsPretend breakpoints.breakpointsPretend
Keywords: manip
Description: Accessor methods for breakpointsPretend objects - not to be called by the user.
URL: ../../../library/tilingArray/html/breakpointsPretend.html

Entry: segmentation
Aliases: segmentation-class confint logLik confint,segmentation-method logLik,segmentation-method plot,segmentation-method show,segmentation-method
Keywords: classes
Description: The class segmentation represents a segmentation result.
URL: ../../../library/tilingArray/html/class-segmentation.html

Entry: comparisonPlot
Aliases: comparisonPlot
Keywords: manip
Description: Plot a vertical layout of panels for the comparison of different along-chromosome profiles.
URL: ../../../library/tilingArray/html/comparisonPlot.html

Entry: costMatrix
Aliases: costMatrix
Keywords: manip
Description: Segmentation cost matrix
URL: ../../../library/tilingArray/html/costMatrix.html

Entry: findSegments
Aliases: findSegments
Keywords: manip
Description: Fit a piecewise constant curve to a sequence of numbers -- OBSOLETE, please use function segment instead.
URL: ../../../library/tilingArray/html/findsegments.html

Entry: normalizeByReference
Aliases: normalizeByReference
Keywords: manip
Description: Probe-specific normalization of hybridization intensities from an oligonucleotide microarray
URL: ../../../library/tilingArray/html/normalizeByReference.html

Entry: otherStrand
Aliases: otherStrand
Keywords: manip
Description: Return the name of the opposite strand
URL: ../../../library/tilingArray/html/otherStrand.html

Entry: plotAlongChrom
Aliases: plotAlongChrom
Keywords: hplot
Description: Plot signals and segmentation for a region of a chromosome
URL: ../../../library/tilingArray/html/plotAlongChrom.html

Entry: plotAlongChromLegend
Aliases: plotAlongChromLegend
Keywords: hplot
Description: Plot a legend for genomic features
URL: ../../../library/tilingArray/html/plotAlongChromLegend.html

Entry: plotFeatures
Aliases: plotFeatures
Keywords: hplot
Description: Plot genomic features for a region along a chromosome
URL: ../../../library/tilingArray/html/plotFeatures.html

Entry: plotSegmentationDots
Aliases: plotSegmentationDots
Keywords: hplot
Description: Plot points for a region along a chromosome
URL: ../../../library/tilingArray/html/plotSegmentationDots.html

Entry: plotSegmentationHeatmap
Aliases: plotSegmentationHeatmap
Keywords: hplot
Description: Plot a heatmap diagram for a region along a chromosome
URL: ../../../library/tilingArray/html/plotSegmentationHeatmap.html

Entry: posMin
Aliases: posMin
Keywords: manip
Description: Find the smallest positive number in a vector
URL: ../../../library/tilingArray/html/posMin.html

Entry: qcPlots
Aliases: qcPlots
Keywords: hplot
Description: Generate simple diagnostic plots for Affymetrix tiling array data
URL: ../../../library/tilingArray/html/qcPlots.html

Entry: readCel2eSet
Aliases: readCel2eSet
Keywords: manip
Description: Read celfiles into an ExpressionSet object.
URL: ../../../library/tilingArray/html/readCel2eSet.html

Entry: sampleStep
Aliases: sampleStep
Keywords: manip
Description: Sampling of ascending numbers to ensure minimal spacing.
URL: ../../../library/tilingArray/html/sampleStep.html

Entry: segChrom
Aliases: segChrom
Keywords: manip
Description: Fit a piecewise constant curve to along chromosome data
URL: ../../../library/tilingArray/html/segChrom.html

Entry: segment
Aliases: segment
Keywords: manip
Description: Fit a piecewise constant curve: segmentation by dynamic programming
URL: ../../../library/tilingArray/html/segment.html

Entry: tilingArray-package
Aliases: tilingArray-package tilingArray
Keywords: package
Description: tilingArray package overview
URL: ../../../library/tilingArray/html/tilingArray-package.html
