tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays

The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.

Author
Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie
Date of publication
None
Maintainer
Zhenyu Xu <zxu@embl.de>
License
Artistic-2.0
Version
1.52.0

View on Bioconductor

Man pages

breakpointsPretend
Accessor methods for breakpointsPretend objects - not to be...
class-segmentation
The class segmentation represents a segmentation result.
comparisonPlot
Plot a vertical layout of panels for the comparison of...
costMatrix
Segmentation cost matrix
findsegments
Fit a piecewise constant curve to a sequence of numbers -...
gffSub
Example of a genomic feature object
normalizeByReference
Probe-specific normalization of hybridization intensities...
otherStrand
Return the name of the opposite strand
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,...
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...
posMin
Find the smallest positive number in a vector
qcPlots
Generate simple diagnostic plots for Affymetrix tiling array...
readCel2eSet
Read celfiles into an ExpressionSet object.
sampleStep
Sampling of ascending numbers to ensure minimal spacing.
segChrom
Fit a piecewise constant curve to along chromosome data...
segment
Fit a piecewise constant curve: segmentation by dynamic...
segnf
Example of a segmentation output object
tilingArray-package
tilingArray package overview

Files in this package

tilingArray/DESCRIPTION
tilingArray/NAMESPACE
tilingArray/R
tilingArray/R/AllClasses.R
tilingArray/R/AllGenerics.R
tilingArray/R/PMindex.R
tilingArray/R/comparisonPlot.R
tilingArray/R/confint.segmentation.R
tilingArray/R/costMatrix.R
tilingArray/R/findsegments.R
tilingArray/R/grid.image.R
tilingArray/R/methods-segmentation.R
tilingArray/R/normalizeByReference.R
tilingArray/R/otherStrand.R
tilingArray/R/plotAlongChrom.R
tilingArray/R/plotAlongChromLegend.R
tilingArray/R/plotPenLL.R
tilingArray/R/plotSegmentationDots.R
tilingArray/R/plotSegmentationHeatmap.R
tilingArray/R/posMin.R
tilingArray/R/qcPlots.R
tilingArray/R/raster.image.R
tilingArray/R/readCel2eSet.R
tilingArray/R/sampleStep.R
tilingArray/R/segChrom.R
tilingArray/R/zzz.R
tilingArray/build
tilingArray/build/vignette.rds
tilingArray/data
tilingArray/data/gffSub.rda
tilingArray/data/segnf.rda
tilingArray/inst
tilingArray/inst/CITATION
tilingArray/inst/doc
tilingArray/inst/doc/assessNorm.Rnw
tilingArray/inst/doc/assessNorm.pdf
tilingArray/inst/doc/costMatrix.Rnw
tilingArray/inst/doc/costMatrix.pdf
tilingArray/inst/doc/findsegments.R
tilingArray/inst/doc/findsegments.Rnw
tilingArray/inst/doc/findsegments.pdf
tilingArray/inst/doc/plotAlongChrom.R
tilingArray/inst/doc/plotAlongChrom.Rnw
tilingArray/inst/doc/plotAlongChrom.pdf
tilingArray/inst/doc/segmentation.Rnw
tilingArray/inst/doc/segmentation.pdf
tilingArray/inst/scripts
tilingArray/inst/scripts/createNormIntensitiesFlatfile.R
tilingArray/inst/scripts/marina.R
tilingArray/inst/scripts/segVariance.Rnw
tilingArray/inst/scripts/testSegmentationConfint.R
tilingArray/inst/vignettes
tilingArray/inst/vignettes/assessNorm.Rnw
tilingArray/inst/vignettes/assessNorm.pdf
tilingArray/inst/vignettes/segmentation.Rnw
tilingArray/inst/vignettes/segmentation.pdf
tilingArray/man
tilingArray/man/PMindex.Rd
tilingArray/man/breakpointsPretend.Rd
tilingArray/man/class-segmentation.Rd
tilingArray/man/comparisonPlot.Rd
tilingArray/man/costMatrix.Rd
tilingArray/man/findsegments.Rd
tilingArray/man/gffSub.Rd
tilingArray/man/normalizeByReference.Rd
tilingArray/man/otherStrand.Rd
tilingArray/man/plotAlongChrom.Rd
tilingArray/man/plotAlongChromLegend.Rd
tilingArray/man/plotFeatures.Rd
tilingArray/man/plotSegmentationDots.Rd
tilingArray/man/plotSegmentationHeatmap.Rd
tilingArray/man/plotpenLL.Rd
tilingArray/man/posMin.Rd
tilingArray/man/qcPlots.Rd
tilingArray/man/readCel2eSet.Rd
tilingArray/man/sampleStep.Rd
tilingArray/man/segChrom.Rd
tilingArray/man/segment.Rd
tilingArray/man/segnf.Rd
tilingArray/man/tilingArray-package.Rd
tilingArray/src
tilingArray/src/findsegments.c
tilingArray/src/sampleStep.c
tilingArray/vignettes
tilingArray/vignettes/Makefile
tilingArray/vignettes/assessNorm.Rnw
tilingArray/vignettes/costMatrix.Rnw
tilingArray/vignettes/findsegments.Rnw
tilingArray/vignettes/plotAlongChrom.Rnw
tilingArray/vignettes/segmentation.Rnw