Man pages for luciansmith/copynumber
Segmentation of single- and multi-track copy number data by penalized least squares regression.
| aspcf | Allele-specific copy number segmentation. |
| 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. |
| 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... |
| plotCircle | Plot a circular genome with aberration frequencies and... |
| plotFreq | Plot percentage of samples with an aberration at a genomic... |
| 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 |
| SNPdata | Artificial SNP array data |
| subsetData | Retrieve a data subset |
| subsetSegments | Retrieve a subset of segments |
| winsorize | Winsorization of copy number data |
