Man pages for pneuvial/c3co
Cancer Cell Clonality using Copy-Number
| alignLoci | Aligns Multiple Copy-Number Data Objects |
| buildSubclones | Build (pure) subclones by resampling real copy-number data |
| c3co | Cancer subclone inference |
| c3coFit-class | Class for the object create by 'fitC3co()' |
| createZdf | Create a data frame to plot subclones |
| FACETSwrapper | Transforms FACETS data and performs a joint segmentation |
| fitC3co | c3co estimation from segment-level copy number data |
| getToyData | Create a toy subclone and mixture data set |
| get.W | Get the matrix of weights W for fixed values of the subclones... |
| get.Zt | Get the matrix of subclones Z for fixed values of the weights... |
| heatmap.3 | Heatmap function |
| initializeZt | Initialization of the latent features of the c3co model |
| loadFACETSdata | Loads FACETS data and transforms them to c3co format |
| loadPSCBSdata | Loads PSCBS data and transforms them into c3co format |
| mixSubclones | Create a mixture of subclones |
| modelFitStatistics | Print statistics of a c3co model |
| modelFitStats | Compute statistics of a c3co model |
| nbrOfChromosomes | Get number of chromosomes |
| nbrOfSamples | Get number of samples |
| nbrOfSegments | Get number of segments |
| posFused-class | Class for the object returned by 'positiveFusedLasso()' |
| positiveFusedLasso | Positive fused Lasso function |
| PSCBSwrapper | Transforms and aligns PSCBS data followed by a joint... |
| pvePlot | Plot Percentage of Variation Explained (PVE) against number... |
| pvePlot2 | Plot Percentage of Variation Explained (PVE) against number... |
| rSparseWeightMatrix | Generate weight matrix |
| rSpMatrix | Generate sparse matrix with at least one non-zero element by... |
| sampleNames | Get sample names |
| segmentData | Joint segmentation |
| trackNames | Get track names |
| Wplot | Plot the weight matrix |
| Zplot | Plot latent profiles along chromosomes |
