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