Name |
Description |
CNInterval |
|
CanvasSegment |
Contains information about a genomic interval. Has functions for computing copy numbers and their likelihoods. |
CanvasVersionInfo |
|
ClusterModel |
Stores information about clustering of CanvasSegment objects |
CnvTypeExtensions |
|
CopyNumberOracle |
This class represents a set of known copy number calls ("truth set"), useful for training models. |
CoverageModel |
|
DensityClusteringModel |
This class implements Density Clustering algorithm introduced in Rodriguez, Alex, and Alessandro Laio. "Clustering by fast search and find of density peaks." Science 344.6191 (2014): 1492-1496. The principle class members are Centroids (Delta in paper) and Rho that are defined as follows: fiven distance matric d[i,j] and distanceThreshold, for each data point i compure Rho(i) = total number of data points within distanceThreshold Centroids(i) = distance of the closes data point of higher density (min(d[i,j] for all j:=Rho(j)>Rho(i))) |
ModelPoint |
Represents a model point in (MAF, Coverage) space |
PloidyInfo |
|
PloidyInterval |
|
SegmentInfo |
Represents a point in (MAF, Coverage) space to be clustered: |
SegmentPloidy |
a SegmentPloidy represents a potential copy number state of a genomic interval. It has a copy number and a major chromosome count. |