Man pages for pneuvial/c3co
Cancer Cell Clonality using Copy-Number

alignLociAligns Multiple Copy-Number Data Objects
buildSubclonesBuild (pure) subclones by resampling real copy-number data
c3coCancer subclone inference
c3coFit-classClass for the object create by 'fitC3co()'
createZdfCreate a data frame to plot subclones
FACETSwrapperTransforms FACETS data and performs a joint segmentation
fitC3coc3co estimation from segment-level copy number data
getToyDataCreate a toy subclone and mixture data set
get.WGet the matrix of weights W for fixed values of the subclones...
get.ZtGet the matrix of subclones Z for fixed values of the weights...
heatmap.3Heatmap function
initializeZtInitialization of the latent features of the c3co model
loadFACETSdataLoads FACETS data and transforms them to c3co format
loadPSCBSdataLoads PSCBS data and transforms them into c3co format
mixSubclonesCreate a mixture of subclones
modelFitStatisticsPrint statistics of a c3co model
modelFitStatsCompute statistics of a c3co model
nbrOfChromosomesGet number of chromosomes
nbrOfSamplesGet number of samples
nbrOfSegmentsGet number of segments
posFused-classClass for the object returned by 'positiveFusedLasso()'
positiveFusedLassoPositive fused Lasso function
PSCBSwrapperTransforms and aligns PSCBS data followed by a joint...
pvePlotPlot Percentage of Variation Explained (PVE) against number...
pvePlot2Plot Percentage of Variation Explained (PVE) against number...
rSparseWeightMatrixGenerate weight matrix
rSpMatrixGenerate sparse matrix with at least one non-zero element by...
sampleNamesGet sample names
segmentDataJoint segmentation
trackNamesGet track names
WplotPlot the weight matrix
ZplotPlot latent profiles along chromosomes
pneuvial/c3co documentation built on May 25, 2019, 10:21 a.m.