aspcf |
Allele-specific copy number segmentation. |
BAF |
Artificial SNP array data |
callAberrations |
Call aberrations in segmented data |
getGRangesFormat |
Get segments on the GRanges format |
imputeMissing |
Impute missing copy number values |
interpolate.pcf |
Interpolation of pcf-estimates. |
logR |
Artificial SNP array data |
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 |