scObject-class: Class "scObject" ~~~

In genome/sciclone: Detect subclones from genomic sequence data

Class "scObject" ~~~

Description

Objects of this class hold data used by the sciClone package, including variant vaf data, copy number calls, clustering results, density and purity calculations, etc.

Objects from the Class

Objects can be created by calls of the form new("scObject").

Slots

vafs.merged:

Object of class "data.frame" a data frame containing variant positions, vafs, cn, clusters, etc

clust:

Object of class "list" a list containing the results of clustering the vafs

densities:

Object of class "list" list containing information on kernel density and peaks

dimensions:

Object of class "numeric" the number of dimensions that are being used for clustering

marginalClust:

Object of class "list" marginal clustering data

sampleNames:

Object of class "character" a vector of names corresponding to the input samples

vafs.1d:

Object of class "list" a list containing 1d vafs and clusters for each sample

ellipse.metadata:

Object of class "list" metadata related to confidence metric plotting

purities:

Object of class "numeric" list of estimated purities for each sample

Methods

No methods defined with class "scObject" in the signature.

genome/sciclone documentation built on Oct. 15, 2023, 5:09 a.m.