Package: tilingArray 1.91.0

Zhenyu Xu

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.

Authors:Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tilingArray/json (API)

# Install 'tilingArray' in R:
install.packages('tilingArray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • gffSub - Example of a genomic feature object
  • segnf - Example of a segmentation output object

On BioConductor:tilingArray-1.91.0(bioc 3.24)tilingArray-1.90.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarrayonechannelpreprocessingvisualization

5.48 score 1 packages 7 scripts 17 mentions 25 exports 65 dependencies

Last updated from:11853d50b3. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

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bioc-checksERROR175
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linux-devel-x86_64NOTE252
source / vignettesOK230
linux-release-arm64NOTE242
linux-release-x86_64NOTE253
macos-release-arm64NOTE132
macos-release-x86_64NOTE397
macos-oldrel-arm64NOTE401
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windows-develNOTE194
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windows-oldrelNOTE176
wasm-releaseOK119

Exports:BGindexbreakpoints.breakpointsPretendcomparisonPlotconfintcostMatrixfindSegmentslogLiknormalizeByReferenceotherStrandplotplotAlongChromplotAlongChromLegendplotFeaturesplotPenLLplotSegmentationDotsplotSegmentationHeatmapPMindexposMinqcPlotsreadCel2eSetresiduals.breakpointsPretendsampleStepsegChromsegmentshow

Dependencies:affyaffyioannotateAnnotationDbiaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfarverfastmapgenefiltergenericsggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpixmappkgconfigpngpreprocessCoreR6RColorBrewerrlangRSQLiteS4VectorsS7sandwichscalesSeqinfostatmodstrucchangesurvivalsysvctrsviridisLitevsnwithrXMLxtableXVectorzoo

Introduction to the plotAlongChrom function
Introduction to the example data | Visualizing the expression profiling with the plotAlongChrom function
Rendered fromplotAlongChrom.Rnwusingutils::Sweave

Last update: 2013-10-24
Started: 2013-10-24

Introduction to using the segment function to fit a piecewise constant curve
Rendered fromfindsegments.Rnwusingutils::Sweave

Last update: 2013-10-24
Started: 2013-10-24

Normalisation with the normalizeByReference function in the tilingArray package
Introduction | Selection of perfect match and background features | Normalization | Alternative normalization methods | Assessment | Version Information
Rendered fromassessNorm.Rnwusingutils::Sweave

Last update: 2013-10-24
Started: 2013-10-24

Segmentation demo
Introduction | Normalization of the data | Segmentation | Visualizing segmentations with the plotAlongChrom function | Version information
Rendered fromsegmentation.Rnwusingutils::Sweave

Last update: 2013-10-24
Started: 2013-10-24

Supplement. Calculation of the cost matrix
Rendered fromcostMatrix.Rnwusingutils::Sweave

Last update: 2013-10-24
Started: 2013-10-24

Readme and manuals

Help Manual

Help pageTopics
tilingArray package overviewtilingArray-package tilingArray
Accessor methods for breakpointsPretend objects - not to be called by the user.breakpoints.breakpointsPretend residuals.breakpointsPretend
Plot a vertical layout of panels for the comparison of different along-chromosome profiles.comparisonPlot
Segmentation cost matrixcostMatrix
Fit a piecewise constant curve to a sequence of numbers - OBSOLETE, please use function segment instead.findSegments
Example of a genomic feature objectgffSub
Probe-specific normalization of hybridization intensities from an oligonucleotide microarraynormalizeByReference
Return the name of the opposite strandotherStrand
Plot signals and segmentation for a region of a chromosomeplotAlongChrom
Plot a legend for genomic featuresplotAlongChromLegend
Plot genomic features for a region along a chromosomeplotFeatures
Plot the log-likelihood and penalized log-likelihoods (AIC, BIC)plotPenLL
Plot points for a region along a chromosomeplotSegmentationDots
Plot a heatmap diagram for a region along a chromosomeplotSegmentationHeatmap
Find the index of the exact match (PM) or background probes from a probeAnno environmentBGindex PMindex
Find the smallest positive number in a vectorposMin
Generate simple diagnostic plots for Affymetrix tiling array dataqcPlots
Read celfiles into an ExpressionSet object.readCel2eSet
Sampling of ascending numbers to ensure minimal spacing.sampleStep
Fit a piecewise constant curve to along chromosome data (wrapper function)segChrom
Fit a piecewise constant curve: segmentation by dynamic programmingsegment
The class segmentation represents a segmentation result.confint confint,segmentation-method logLik logLik,segmentation-method plot,segmentation,ANY-method segmentation-class show,segmentation-method
Example of a segmentation output objectsegnf