tilingArray: Transcript mapping with high-density oligonucleotide tiling arrays
Version 1.54.0

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.

AuthorWolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie
Bioconductor views Microarray OneChannel Preprocessing Visualization
Date of publicationNone
MaintainerZhenyu Xu <zxu@embl.de>
LicenseArtistic-2.0
Version1.54.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("tilingArray")

Getting started

Package overview

Popular man pages

findsegments: Fit a piecewise constant curve to a sequence of numbers -...
gffSub: Example of a genomic feature object
plotAlongChrom: Plot signals and segmentation for a region of a chromosome
plotpenLL: Plot the log-likelihood and penalized log-likelihoods (AIC,...
plotSegmentationDots: Plot points for a region along a chromosome
PMindex: Find the index of the exact match (PM) or background probes...
qcPlots: Generate simple diagnostic plots for Affymetrix tiling array...
See all...

All man pages Function index File listing

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

Functions

BGindex Man page Source code
PMindex Man page Source code
alongChromTicks Source code
breakpoints.breakpointsPretend Man page Source code
comparisonPlot Man page Source code
confint Man page
confint,segmentation-method Man page
costMatrix Man page Source code
featureColors Source code
findSegments Man page Source code
gffSub Man page
grid.image Source code
interpolateZ Source code
logLik Man page
logLik,segmentation-method Man page
matDensities Source code
myPixmap Source code
myWrite Source code
newVP Source code
normalizeByReference Man page Source code
onAttach Source code
otherStrand Man page Source code
plot,segmentation,ANY-method Man page
plotAlongChrom Man page Source code
plotAlongChromLegend Man page Source code
plotFeatures Man page Source code
plotPenLL Man page Source code
plotSegmentationDots Man page Source code
plotSegmentationHeatmap Man page Source code
posMin Man page Source code
qcPlots Man page Source code
raster.image Source code
readCel2eSet Man page Source code
residuals.breakpointsPretend Man page Source code
sampleStep Man page Source code
segChrom Man page Source code
segment Man page Source code
segmentation-class Man page
segnf Man page
show,segmentation-method Man page
tilingArray Man page
tilingArray-package Man page
validSegmentation Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/PMindex.R
R/comparisonPlot.R
R/confint.segmentation.R
R/costMatrix.R
R/findsegments.R
R/grid.image.R
R/methods-segmentation.R
R/normalizeByReference.R
R/otherStrand.R
R/plotAlongChrom.R
R/plotAlongChromLegend.R
R/plotPenLL.R
R/plotSegmentationDots.R
R/plotSegmentationHeatmap.R
R/posMin.R
R/qcPlots.R
R/raster.image.R
R/readCel2eSet.R
R/sampleStep.R
R/segChrom.R
R/zzz.R
build
build/vignette.rds
data
data/gffSub.rda
data/segnf.rda
inst
inst/CITATION
inst/doc
inst/doc/assessNorm.Rnw
inst/doc/assessNorm.pdf
inst/doc/costMatrix.Rnw
inst/doc/costMatrix.pdf
inst/doc/findsegments.R
inst/doc/findsegments.Rnw
inst/doc/findsegments.pdf
inst/doc/plotAlongChrom.R
inst/doc/plotAlongChrom.Rnw
inst/doc/plotAlongChrom.pdf
inst/doc/segmentation.Rnw
inst/doc/segmentation.pdf
inst/scripts
inst/scripts/createNormIntensitiesFlatfile.R
inst/scripts/marina.R
inst/scripts/segVariance.Rnw
inst/scripts/testSegmentationConfint.R
inst/vignettes
inst/vignettes/assessNorm.Rnw
inst/vignettes/assessNorm.pdf
inst/vignettes/segmentation.Rnw
inst/vignettes/segmentation.pdf
man
man/PMindex.Rd
man/breakpointsPretend.Rd
man/class-segmentation.Rd
man/comparisonPlot.Rd
man/costMatrix.Rd
man/findsegments.Rd
man/gffSub.Rd
man/normalizeByReference.Rd
man/otherStrand.Rd
man/plotAlongChrom.Rd
man/plotAlongChromLegend.Rd
man/plotFeatures.Rd
man/plotSegmentationDots.Rd
man/plotSegmentationHeatmap.Rd
man/plotpenLL.Rd
man/posMin.Rd
man/qcPlots.Rd
man/readCel2eSet.Rd
man/sampleStep.Rd
man/segChrom.Rd
man/segment.Rd
man/segnf.Rd
man/tilingArray-package.Rd
src
src/findsegments.c
src/sampleStep.c
vignettes
vignettes/Makefile
vignettes/assessNorm.Rnw
vignettes/costMatrix.Rnw
vignettes/findsegments.Rnw
vignettes/plotAlongChrom.Rnw
vignettes/segmentation.Rnw
tilingArray documentation built on May 20, 2017, 10:43 p.m.

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