Transcript mapping with high-density oligonucleotide tiling arrays

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Documentation for package ‘tilingArray’ version 1.30.0

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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