Package index
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logRBAF - Artificial SNP array data
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aspcf() - Allele-specific copy number segmentation.
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callAberrations() - Call aberrations in segmented data
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copynumbercopynumber-package - copynumber: Segmentation of Single- and Multi-Track Copy Number Data by Penalized Least Squares Regression (with hg38, mm10, and mm39)
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getGRangesFormat() - Get segments on the GRanges format
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imputeMissing() - Impute missing copy number values
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interpolate.pcf() - Interpolation of pcf-estimates.
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lymphoma - 3K aCGH data
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micma - Subset of 244K aCGH data
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multipcf() - Multi-sample copy number segmentation.
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pcf() - Single-sample copy number segmentation.
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pcfPlain() - Plain single-sample copy number segmentation.
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plotAberration() - Plot areas with copy number aberrations
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plotAllele() - Plot SNP data and/or aspcf segmentation results
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plotChrom() - Plot copy number data and/or segmentation results by chromosome
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plotCircle() - Plot a circular genome with aberration frequencies and connections between genomic loci added.
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plotFreq() - Plot percentage of samples with an aberration at a genomic position
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plotGamma() - Plot segmentation results for several values of gamma
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plotGenome() - Plot copy number data and/or segmentation results
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plotHeatmap() - Plot copy number heatmap
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plotSample() - Plot copy number data and/or segmentation results by sample
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selectSegments() - Select multipcf segments
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subsetData() - Retrieve a data subset
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subsetSegments() - Retrieve a subset of segments
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winsorize() - Winsorization of copy number data