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.

AuthorWolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie
Date of publicationNone
MaintainerZhenyu Xu <zxu@embl.de>
LicenseArtistic-2.0
Version1.52.0

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

Functions

BGindex Man page
breakpoints.breakpointsPretend Man page
comparisonPlot Man page
confint Man page
confint,segmentation-method Man page
costMatrix Man page
findSegments Man page
gffSub Man page
logLik Man page
logLik,segmentation-method Man page
normalizeByReference Man page
otherStrand Man page
plotAlongChrom Man page
plotAlongChromLegend Man page
plotFeatures Man page
plotPenLL Man page
plot,segmentation,ANY-method Man page
plotSegmentationDots Man page
plotSegmentationHeatmap Man page
PMindex Man page
posMin Man page
qcPlots Man page
readCel2eSet Man page
residuals.breakpointsPretend Man page
sampleStep Man page
segChrom Man page
segment Man page
segmentation-class Man page
segnf Man page
show,segmentation-method Man page
tilingArray Man page
tilingArray-package Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.